Is CCL5 p.Ala5Val (c.14C>T) pathogenic?

CCL5 p.Ala5Val (c.14C>T) is classified Likely benign in CCL5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-03). AlphaMissense: likely benign (0.0936); Ultra-rare (popmax 0.0165%, mid).

How common is CCL5 p.Ala5Val (c.14C>T) in the general population?

CCL5 p.Ala5Val (c.14C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

What do computational predictors say about CCL5 p.Ala5Val (c.14C>T)?

AlphaMissense predicts likely benign (score 0.0936) — an in-silico prediction, not a clinical call.

CCL5 p.Ala5Val

c.14C>T · rs571565063 · VCV2379782

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0936 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0936	likely benign
REVEL	0.031	moderately benign-leaning
SaProt	LLR -7.41	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP -3.4, phastCons 0.003
Overall
CADD	11.97	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,062 alleles

Filtering AF 0.00516% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00377%

Overall 0.00174% 28/1,612,550 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,062
South Asian	0.00993%	10,069
African / African-American	0.00533%	18,753
East Asian	0.00223%	44,836
European (non-Finnish)	0.0011%	90,719

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: CCL5
Protein: p.Ala5Val
Coding: c.14C>T
MANE Select: NM_002985
dbSNP: rs571565063
Type: single nucleotide variant
Location: chr17:35880292 (GRCh38)
Gene constraint: LOEUF 1.387 · pLI 0.15 (gnomAD)
Structure: AlphaFold pLDDT 89.51 · 23 PDB

Full CCL5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCL5 p.Arg40His Uncertain significance ★ ⚠ same type
CCL5 p.Arg70His Uncertain significance ★ ⚠ same type
CCL5 p.Arg82Gln Uncertain significance ★ ⚠ same type
CCL5 p.Cys33Arg Uncertain significance ★ ⚠ same type
CCL5 p.Lys68Arg Uncertain significance ★ ⚠ same type
CCL5 p.Ser28Leu Uncertain significance ★ ⚠ same type
CCL5 p.Ser58Phe Uncertain significance ★ ⚠ same type
CCL5 p.Thr30Ala 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/ccl5-p-ala5val (accessed [today's date]).

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