Is DLGAP2 c.2949+5G>C pathogenic?

DLGAP2 c.2949+5G>C is classified Likely benign in DLGAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-28). Rare (popmax 0.138%, afr); Associated with DLGAP2-related disorder.

What condition is associated with DLGAP2 c.2949+5G>C?

DLGAP2 c.2949+5G>C is associated with DLGAP2-related disorder (ClinVar).

How common is DLGAP2 c.2949+5G>C in the general population?

DLGAP2 c.2949+5G>C is rare (popmax 0.138%, afr) (gnomAD).

DLGAP2 c.2949+5G>C

rs77345811 · VCV3058684

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.138%, afr)

Conditions

DLGAP2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +5	donor splice region (+5, within the first 6 intronic nt) · inside the BP7-excluded zone
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.5	GERP -4.1
Overall
CADD	2.027	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.138% African / African-American · 103/74,654 alleles

Filtering AF 0.116% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.108%

Overall 0.00807% 129/1,597,754 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.138%	725
Remaining individualsnot grpmax-eligible	0.0178%	5,613
Admixed American	0.0171%	5,841
European (non-Finnish)	0.000427%	234,094

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: DLGAP2
Coding: c.2949+5G>C
MANE Select: NM_001346810
dbSNP: rs77345811
Type: single nucleotide variant
Location: chr8:1697304 (GRCh38)
Gene constraint: LOEUF 0.425 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 48.83

Full DLGAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DLGAP2-related disorder

Similar variants

DLGAP2 p.Glu892Gln Uncertain significance ★ ⚠ same condition
DLGAP2 p.Asn662Thr Uncertain significance ⚠ same condition
DLGAP2 p.Leu192Val Uncertain significance ⚠ same condition
DLGAP2 p.Ser85Cys Uncertain significance ⚠ same condition
DLGAP2 c.107-10G>C Likely benign same condition
DLGAP2 c.1231-10C>G Likely benign same condition
DLGAP2 c.1810+10C>T Likely benign same condition
DLGAP2 c.2202+9C>T Likely benign same condition

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/dlgap2-c-2949-plus-5g-c (accessed [today's date]).

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