Is BABAM1 p.Ser72= (c.216C>T) pathogenic?

BABAM1 p.Ser72= (c.216C>T) is classified Likely benign in BABAM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-02). Rare (popmax 0.131%, sas).

How common is BABAM1 p.Ser72= (c.216C>T) in the general population?

BABAM1 p.Ser72= (c.216C>T) is rare (popmax 0.131%, sas) (gnomAD).

BABAM1 p.Ser72=

c.216C>T · VCV4645020

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.131%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.048	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.045	GERP 0.9, phastCons 0.74
Overall
CADD	6.919	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.131% South Asian · 115/87,894 alleles

Filtering AF 0.111% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.104%

Overall 0.00772% 123/1,593,280 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.131%	764
Middle Eastern	0.0209%	4,786
Remaining individualsnot grpmax-eligible	0.00325%	30,780
European (non-Finnish)	0.000427%	234,258

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: BABAM1
Protein: p.Ser72=
Coding: c.216C>T
MANE Select: NM_014173
Type: single nucleotide variant
Location: chr19:17269022 (GRCh38)
Gene constraint: LOEUF 0.672 · pLI 0.13 (gnomAD)
Structure: AlphaFold pLDDT 79.21 · 10 PDB
Residue 72: the 'disordered' region

Full BABAM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BABAM1 c.-13-45C>T Benign ★★ same type
BABAM1 p.Ala283Thr Uncertain significance ★ ⚠ same type
BABAM1 p.Arg212His Uncertain significance ★ ⚠ same type
BABAM1 p.Arg212Pro Uncertain significance ★ ⚠ same type
BABAM1 p.Arg219Cys Uncertain significance ★ ⚠ same type
BABAM1 p.Arg26Cys Uncertain significance ★ ⚠ same type
BABAM1 p.Arg85Gln Uncertain significance ★ ⚠ same type
BABAM1 p.Asn122Ser 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/babam1-p-ser72 (accessed [today's date]).

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