Is MYB p.Ser250= (c.750T>C) pathogenic?

MYB p.Ser250= (c.750T>C) is classified Benign in MYB (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Low-frequency (popmax 1.34%, nfe).

How common is MYB p.Ser250= (c.750T>C) in the general population?

MYB p.Ser250= (c.750T>C) is low-frequency (popmax 1.34%, nfe) (gnomAD).

MYB p.Ser250=

c.750T>C · rs61756670 · VCV777172

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.34%, nfe)

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 -1.2	GERP -3.9, phastCons 0.002
Overall
CADD	6.82	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.34% European (non-Finnish) · 15,867/1,179,812 alleles

Filtering AF 1.33% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.32%

Overall 1.11% 17,971/1,614,006 alleles · low-frequency

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	2.19%	46
Finnishnot grpmax-eligible	1.66%	60
European (non-Finnish)grpmax	1.34%	74
Remaining individualsnot grpmax-eligible	0.746%	134
Middle Eastern	0.412%	242
South Asian	0.229%	436
Admixed American	0.223%	448
African / African-American	0.197%	507
Ashkenazi Jewishnot grpmax-eligible	0.118%	846
East Asian	0.00223%	44,888

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: MYB
Protein: p.Ser250=
Coding: c.750T>C
MANE Select: NM_001130173
dbSNP: rs61756670
Type: single nucleotide variant
Location: chr6:135192546 (GRCh38)
Gene constraint: LOEUF 0.443 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 59.16

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

Similar variants

MYB p.Thr589= Benign/Likely benign ★★ same type
MYB p.Ala278Thr Uncertain significance ★ ⚠ same type
MYB p.Ala470Ser Uncertain significance ★ same type
MYB p.Ala491Asp Uncertain significance ★ same type
MYB p.Ala719Glu Uncertain significance ★ ⚠ same type
MYB p.Arg337Gly Uncertain significance ★ ⚠ same type
MYB p.Arg484Trp Uncertain significance ★ same type
MYB p.Arg4Ser Uncertain significance ★ ⚠ 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/myb-p-ser250 (accessed [today's date]).

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