Is ELN c.1747+93C>A pathogenic?

ELN c.1747+93C>A is classified Uncertain significance in ELN (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-02). AlphaMissense: likely benign (0.0788); Absent from gnomAD v4.1.

How common is ELN c.1747+93C>A in the general population?

ELN c.1747+93C>A is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ELN c.1747+93C>A?

AlphaMissense predicts likely benign (score 0.0788) — an in-silico prediction, not a clinical call.

ELN c.1747+93C>A

rs1554683829 · VCV1314459

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0788 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0788	likely benign
REVEL	0.003	strongly benign-leaning
SaProt	LLR -8.03	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
Splice region	donor +93	deep intronic (+93 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.23	GERP -2.1
Non-coding constraint	Z 0.99	1 kb window · o/e 0.93 · regional · uncalibrated
Overall
CADD	3.828	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ELN
Coding: c.1747+93C>A
MANE Select: NM_000501
dbSNP: rs1554683829
Type: single nucleotide variant
Location: chr7:74060594 (GRCh38)
Gene constraint: LOEUF 0.696 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 36.20

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

Similar variants

ELN c.134-1G>A Likely pathogenic ★★ same type
ELN c.377-2A>G Pathogenic/Likely pathogenic ★★ same type
ELN c.643+1G>A Pathogenic/Likely pathogenic ★★ same type
ELN c.643+1G>C Likely pathogenic ★★ same type
ELN c.686-2A>G Likely pathogenic ★★ same type
ELN c.800-1G>A Pathogenic/Likely pathogenic ★★ same type
ELN c.800-2A>G Pathogenic ★★ same type
ELN c.800-3C>G 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/eln-c-1747-plus-93c-a (accessed [today's date]).

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