Is CD151 c.84+13C>T pathogenic?

CD151 c.84+13C>T is classified Benign/Likely benign in CD151 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-27). Rare (popmax 0.326%, nfe).

How common is CD151 c.84+13C>T in the general population?

CD151 c.84+13C>T is rare (popmax 0.326%, nfe) (gnomAD).

CD151 c.84+13C>T

rs201750899 · VCV1175013

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.326%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +13	near-intronic (+13 nt from the splice site)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.3	GERP -2.4
Overall
CADD	2.616	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.326% European (non-Finnish) · 3,801/1,164,482 alleles

Filtering AF 0.318% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.314%

Overall 0.264% 4,217/1,595,278 alleles · rare

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	4.41%	23
European (non-Finnish)grpmax	0.326%	306
Remaining individualsnot grpmax-eligible	0.186%	538
South Asian	0.158%	634
African / African-American	0.0763%	1,311
Middle Eastern	0.051%	1,959
Finnishnot grpmax-eligible	0.0432%	2,317
Admixed American	0.0351%	2,853
Ashkenazi Jewishnot grpmax-eligible	0.0339%	2,952

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: CD151
Coding: c.84+13C>T
MANE Select: NM_004357
dbSNP: rs201750899
Type: single nucleotide variant
Location: chr11:836166 (GRCh38)
Gene constraint: LOEUF 0.816 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.02

Full CD151 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD151 p.Lys7Ter Pathogenic ★★ same type
CD151 c.352-11C>G Uncertain significance ★★ same type
CD151 c.702+4A>G Uncertain significance ★★ same type
CD151 c.702+5G>C Uncertain significance ★★ same type
CD151 p.Ala145Thr Uncertain significance ★★ ⚠ same type
CD151 p.Ala81Thr Uncertain significance ★★ ⚠ same type
CD151 p.Arg133Cys Uncertain significance ★★ ⚠ same type
CD151 p.Arg165Gln 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/cd151-c-84-plus-13c-t (accessed [today's date]).

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