Is BCR p.Ser202= (c.606C>T) pathogenic?

BCR p.Ser202= (c.606C>T) is classified Benign/Likely benign in BCR (ClinVar, Multiple submitters, 3 submitters; last evaluated 2022-04-05). Low-frequency (popmax 2.04%, afr); Associated with chronic myeloid leukemia.

What condition is associated with BCR p.Ser202= (c.606C>T)?

BCR p.Ser202= (c.606C>T) is associated with chronic myeloid leukemia, acute lymphoblastic leukemia (ClinVar).

How common is BCR p.Ser202= (c.606C>T) in the general population?

BCR p.Ser202= (c.606C>T) is low-frequency (popmax 2.04%, afr) (gnomAD).

How is Chronic myeloid leukemia inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

BCR p.Ser202=

c.606C>T · rs147507158 · VCV780633

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.04%, afr)

Conditions

chronic myeloid leukemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.2	GERP -3.8
Overall
CADD	5.326	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.04% African / African-American · 1,530/75,064 alleles

Filtering AF 1.95% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.92%

Overall 0.12% 1,933/1,612,976 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.04%	49
Middle Eastern	0.231%	433
Admixed American	0.222%	451
Remaining individualsnot grpmax-eligible	0.157%	638
Ashkenazi Jewishnot grpmax-eligible	0.0372%	2,691
European (non-Finnish)	0.0119%	8,429
South Asian	0.00769%	13,012

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BCR
Protein: p.Ser202=
Coding: c.606C>T
MANE Select: NM_004327
dbSNP: rs147507158
Type: single nucleotide variant
Location: chr22:23181566 (GRCh38)
Gene constraint: LOEUF 0.608 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 65.61 · 5 PDB
Residue 202: a modified residue (phosphoserine); the 'kinase' region; the 'disordered' region; the 'binding to abl sh2-domain' region

Full BCR gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

chronic myeloid leukemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: acute lymphoblastic leukemia

For Chronic myeloid leukemia (Orphanet):

Inheritance: Not applicable
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

BCR p.Ala786Thr Uncertain significance ★ ⚠ same condition
BCR p.Pro229Ser Uncertain significance ★ ⚠ same condition
BCR p.Pro383= Uncertain significance ★ same condition
BCR p.Val1094fs Conflicting classifications of pathogenicity ★ same condition
BCR p.Ser356Arg Uncertain significance ★★ ⚠ same type
BCR c.2116-6C>G Benign/Likely benign ★★ same type
BCR c.2116-7C>A Benign/Likely benign ★★ same type
BCR c.2526+7G>T Benign/Likely benign ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bcr-p-ser202 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown