Is DCDC2 c.293+79C>T pathogenic?

DCDC2 c.293+79C>T is classified Likely benign in DCDC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-06-16). Low-frequency (popmax 4.29%, afr).

How common is DCDC2 c.293+79C>T in the general population?

DCDC2 c.293+79C>T is low-frequency (popmax 4.29%, afr) (gnomAD).

DCDC2 c.293+79C>T

rs140803474 · VCV683196

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 4.29%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +79	deep intronic (+79 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.099	GERP -1.6, phastCons 0.008
Non-coding constraint	Z 2.87	1 kb window · o/e 0.82 · regional · uncalibrated
Overall
CADD	0.606	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.29% African / African-American · 3,052/71,096 alleles

Filtering AF 4.17% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.11%

Overall 2.33% 34,139/1,468,030 alleles · low-frequency

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	8.55%	12
African / African-Americangrpmax	4.29%	23
European (non-Finnish)	2.63%	38
Remaining individualsnot grpmax-eligible	2.08%	48
Admixed American	1.14%	88
Ashkenazi Jewishnot grpmax-eligible	0.688%	145
Finnishnot grpmax-eligible	0.475%	210
Middle Eastern	0.285%	351
South Asian	0.0258%	3,870
East Asian	0.00461%	21,669

Amish 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: DCDC2
Coding: c.293+79C>T
MANE Select: NM_016356
dbSNP: rs140803474
Type: single nucleotide variant
Location: chr6:24357379 (GRCh38)
Gene constraint: LOEUF 1.062 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.93 · 1 PDB

Full DCDC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCDC2 c.294-2A>G Pathogenic ★★ same type
DCDC2 c.349-2A>G Pathogenic ★★ same type
DCDC2 c.705-2A>G Pathogenic ★★ same type
DCDC2 p.Leu297Ter Pathogenic ★★ same type
DCDC2 p.Met1Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
DCDC2 p.Ser128Ter Pathogenic/Likely pathogenic ★★ same type
DCDC2 p.Ala153Gly Uncertain significance ★★ ⚠ same type
DCDC2 p.Ala356Pro 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/dcdc2-c-293-plus-79c-t (accessed [today's date]).

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