Is C7 p.Glu615del (c.1842AGA[1]) pathogenic?

C7 p.Glu615del (c.1842AGA[1]) is classified Uncertain significance in C7 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-08). Very rare (popmax 0.00223%, eas).

How common is C7 p.Glu615del (c.1842AGA[1]) in the general population?

C7 p.Glu615del (c.1842AGA[1]) is very rare (popmax 0.00223%, eas) (gnomAD).

C7 p.Glu615del

c.1842AGA[1] · rs2478244884 · VCV2003403

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.8	GERP 2.9, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,880 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000479% 7/1,461,448 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,880
Remaining individualsnot grpmax-eligible	0.0016%	62,480
European (non-Finnish)	0.000424%	235,938

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: C7
Protein: p.Glu615del
Coding: c.1842AGA[1]
MANE Select: NM_001565 · reported on NM_000587
dbSNP: rs2478244884
Type: Microsatellite
Location: chr5:40964833 (GRCh38)
Structure: AlphaFold pLDDT 89.67 · 6 PDB

Full C7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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C7 p.Leu286fs Pathogenic ★ same type
C7 p.Pro135del Uncertain significance ★ same type
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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/c7-p-glu615del (accessed [today's date]).

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