Is BARD1 p.Ser16= (c.48C>A) pathogenic?

BARD1 p.Ser16= (c.48C>A) is classified Likely benign in BARD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-01-26). No allele count reported in gnomAD v4.1 (AN 1,592,442); Associated with hereditary neoplastic syndrome.

What condition is associated with BARD1 p.Ser16= (c.48C>A)?

BARD1 p.Ser16= (c.48C>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BARD1 p.Ser16= (c.48C>A) in the general population?

BARD1 p.Ser16= (c.48C>A) is no allele count reported in gnomAD v4.1 (AN 1,592,442) (gnomAD).

BARD1 p.Ser16=

c.48C>A · rs770753803 · VCV1743929

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,592,442)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -2.8	GERP -3.5
Overall
CADD	4.155	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,592,442). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BARD1
Protein: p.Ser16=
Coding: c.48C>A
MANE Select: NM_000465
dbSNP: rs770753803
Type: single nucleotide variant
Location: chr2:214809522 (GRCh38)
Gene constraint: LOEUF 1.087 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 64.82 · 11 PDB
Residue 16: the 'disordered' region

Full BARD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BARD1 p.Ser16Cys Uncertain significance ★★ ⚠ same residue
BARD1 p.Ser16Phe Uncertain significance ★★ same residue
BARD1 p.Ser16Tyr Uncertain significance ★★ ⚠ same residue
BARD1 p.Ser16Ala Uncertain significance ★ ⚠ same residue
BARD1 c.1314+1G>A Pathogenic/Likely pathogenic ★★ same condition
BARD1 c.1314+1G>T Likely pathogenic ★★ same condition
BARD1 c.1396-1G>A Likely pathogenic ★★ same condition
BARD1 c.1396-1G>C Likely pathogenic ★★ same condition

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/bard1-p-ser16 (accessed [today's date]).

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