Is BBS2 c.*13C>T pathogenic?

BBS2 c.13C>T is classified Benign/Likely benign in BBS2 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2024-11-14). Common (popmax 6.32%, amr) — too common for a highly-penetrant pathogenic allele; Associated with Bardet-Biedl syndrome 2.

What condition is associated with BBS2 c.*13C>T?

BBS2 c.*13C>T is associated with Bardet-Biedl syndrome 2 (ClinVar).

How is Bardet-Biedl syndrome inherited?

Typically Autosomal recessive, Oligogenic (Orphanet). A genetic counselor can assess individual risk for a family.

BBS2 c.*13C>T

Q: How common is BBS2 c.*13C>T in the general population?

BBS2 c.*13C>T is common (popmax 6.32%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs141170836 · VCV261976

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Common

common (popmax 6.32%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

Bardet-Biedl syndrome 2

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 -5.5	GERP -3.2
Non-coding constraint	Z 1.24	1 kb window · o/e 0.90 · regional · uncalibrated
Overall
CADD	0.029	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.32% Admixed American · 3,785/59,932 alleles

Filtering AF 6.15% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.08%

Overall 0.387% 6,231/1,609,052 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	6.32%	16
East Asian	2.71%	37
Finnishnot grpmax-eligible	0.93%	107
Remaining individualsnot grpmax-eligible	0.443%	226
African / African-American	0.0734%	1,362
South Asian	0.0583%	1,716
Ashkenazi Jewishnot grpmax-eligible	0.0542%	1,846
Middle Eastern	0.033%	3,026
European (non-Finnish)	0.02%	5,003

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: BBS2
Coding: c.*13C>T
MANE Select: NM_031885
dbSNP: rs141170836
Type: single nucleotide variant
Location: chr16:56484748 (GRCh38)
Gene constraint: LOEUF 0.892 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.49

Full BBS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Bardet-Biedl syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Bardet-Biedl syndrome (Orphanet):

Inheritance: Autosomal recessive, Oligogenic
Onset: Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Specific population)

Similar variants

BBS2 c.118-1G>T Likely pathogenic ★★ same condition
BBS2 c.118-2A>C Likely pathogenic ★★ same condition
BBS2 c.118-2A>G Likely pathogenic ★★ same condition
BBS2 c.1225+2T>C Likely pathogenic ★★ same condition
BBS2 c.1225+2T>G Likely pathogenic ★★ same condition
BBS2 c.1397+1G>A Pathogenic/Likely pathogenic ★★ same condition
BBS2 c.1397+2T>C Likely pathogenic ★★ same condition
BBS2 c.1398-2A>G 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/bbs2-c-star-13c-t (accessed [today's date]).

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