Is DPF2 c.301+3A>G pathogenic?

DPF2 c.301+3A>G is classified Benign in DPF2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-06-01). Low-frequency (popmax 1.27%, nfe).

How common is DPF2 c.301+3A>G in the general population?

DPF2 c.301+3A>G is low-frequency (popmax 1.27%, nfe) (gnomAD).

DPF2 c.301+3A>G

rs2307267 · VCV1530606

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.27%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +3	donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone
SpliceAI	<0.2	all four deltas below 0.2 · A>C here scores Δ0.83 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.4	GERP 0.086, phastCons 0.99
Non-coding constraint	Z 0.70	1 kb window · o/e 0.95 · regional · uncalibrated
Overall
CADD	17.47	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.27% European (non-Finnish) · 14,957/1,179,978 alleles

Filtering AF 1.25% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.24%

Overall 1.12% 18,080/1,613,944 alleles · low-frequency

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	2.98%	34
European (non-Finnish)grpmax	1.27%	79
Remaining individualsnot grpmax-eligible	0.947%	106
Amishnot grpmax-eligible	0.768%	130
Admixed American	0.368%	272
South Asian	0.226%	442
African / African-American	0.184%	544
Ashkenazi Jewishnot grpmax-eligible	0.172%	581
Middle Eastern	0.0825%	1,212
East Asian	0.00223%	44,888

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: DPF2
Coding: c.301+3A>G
MANE Select: NM_006268
dbSNP: rs2307267
Type: single nucleotide variant
Location: chr11:65341076 (GRCh38)
Gene constraint: LOEUF 0.287 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 69.62 · 9 PDB

Full DPF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DPF2 c.904+1G>A Pathogenic ★★ same type
DPF2 p.Arg350His Pathogenic/Likely pathogenic ★★ same type
DPF2 p.Asp346Asn Likely pathogenic ★★ same type
DPF2 p.Asp349Asn Pathogenic/Likely pathogenic ★★ same type
DPF2 p.Ala133Pro Uncertain significance ★★ ⚠ same type
DPF2 p.Arg38His Uncertain significance ★★ ⚠ same type
DPF2 p.Arg77Gln Uncertain significance ★★ ⚠ same type
DPF2 p.Arg83Trp 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/dpf2-c-301-plus-3a-g (accessed [today's date]).

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