Is DLD c.*18del pathogenic?

DLD c.18del is classified Benign in DLD (ClinVar, Single submitter, 1 submitter; last evaluated 2013-12-23). Very rare (popmax 0.00224%, eas).

How common is DLD c.*18del in the general population?

DLD c.*18del is very rare (popmax 0.00224%, eas) (gnomAD).

DLD c.*18del

rs796051946 · VCV203673

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00224%, 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 0.21	GERP 0.26
Non-coding constraint	Z 1.73	1 kb window · o/e 0.83 · regional · uncalibrated

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00224% East Asian · 1/44,638 alleles

Filtering AF 0.000436% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000318%

Overall 0.00105% 15/1,433,782 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00502%	19,935
East Asiangrpmax	0.00224%	44,638
Admixed American	0.00168%	59,700
European (non-Finnish)	0.000861%	116,093

Finnish 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: DLD
Coding: c.*18del
MANE Select: NM_000108
dbSNP: rs796051946
Type: Deletion
Location: chr7:107919277 (GRCh38)
Gene constraint: LOEUF 0.727 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.69 · 17 PDB

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

Similar variants

DLD p.Gln268fs Pathogenic/Likely pathogenic ★★ same type
DLD p.Gly137del Pathogenic/Likely pathogenic ★★ same type
DLD p.Gly246fs Likely pathogenic ★★ same type
DLD p.Thr34_Tyr35insTer Pathogenic/Likely pathogenic ★★ same type
DLD p.Tyr473fs Pathogenic ★★ same type
DLD p.Asp121fs Pathogenic ★ same type
DLD p.Asp286fs Likely pathogenic ★ same type
DLD p.Asp368fs Likely pathogenic ★ 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/dld-c-star-18del (accessed [today's date]).

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