Is CD320 c.142+180C>A pathogenic?

CD320 c.142+180C>A is classified Benign in CD320 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-06-23). Common (popmax 5.61%, afr) — too common for a highly-penetrant pathogenic allele.

CD320 c.142+180C>A

Q: How common is CD320 c.142+180C>A in the general population?

CD320 c.142+180C>A is common (popmax 5.61%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs137914824 · VCV1225417

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 5.61%, afr) — 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 +180	deep intronic (+180 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.49	GERP 0.88
Non-coding constraint	Z -0.23	1 kb window · o/e 1.02 · regional · uncalibrated
Overall
CADD	2.942	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.61% African / African-American · 2,332/41,572 alleles

Filtering AF 5.42% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.34%

Overall 1.59% 2,421/152,308 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.61%	18
Remaining individualsnot grpmax-eligible	0.853%	117
Admixed American	0.418%	239
European (non-Finnish)	0.0103%	9,717

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.142+180C>A
MANE Select: NM_016579
dbSNP: rs137914824
Type: single nucleotide variant
Location: chr19:8307969 (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-142-plus-180c-a (accessed [today's date]).

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