Is CD320 c.502+297C>A pathogenic?

CD320 c.502+297C>A is classified Benign in CD320 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-07). Common (popmax 67.4%, nfe) — too common for a highly-penetrant pathogenic allele.

CD320 c.502+297C>A

Q: How common is CD320 c.502+297C>A in the general population?

CD320 c.502+297C>A is common (popmax 67.4%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs2913943 · VCV1231182

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 67.4%, nfe) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +297	deep intronic (+297 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.45	GERP -0.4
Overall
CADD	1.149	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 67.4% European (non-Finnish) · 45,823/67,946 alleles

Filtering AF 66.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 66.7%

Overall 55.2% 83,904/151,958 alleles · common

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	69.6%	1
European (non-Finnish)grpmax	67.4%	1
Amishnot grpmax-eligible	65.6%	2
South Asian	58.3%	2
Middle Eastern	57.8%	2
Ashkenazi Jewishnot grpmax-eligible	57.7%	2
Remaining individualsnot grpmax-eligible	52.9%	2
Admixed American	49.5%	2
East Asian	46.2%	2
African / African-American	34%	3

Finnish 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: CD320
Coding: c.502+297C>A
MANE Select: NM_016579
dbSNP: rs2913943
Type: single nucleotide variant
Location: chr19:8303558 (GRCh38)
Gene constraint: LOEUF 1.488 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.61 · 6 PDB

Full CD320 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD320 p.Arg129Leu Uncertain significance ★★ ⚠ same type
CD320 p.Arg138Ser Uncertain significance ★★ ⚠ same type
CD320 p.Arg254Gln Uncertain significance ★★ ⚠ same type
CD320 p.Arg258His Uncertain significance ★★ ⚠ same type
CD320 p.Asn170Ser Uncertain significance ★★ ⚠ same type
CD320 p.Asp143Asn Uncertain significance ★★ ⚠ same type
CD320 p.Asp160Asn Uncertain significance ★★ ⚠ same type
CD320 p.Gly166Val 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/cd320-c-502-plus-297c-a (accessed [today's date]).

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