Is HTT c.747+4del pathogenic?

HTT c.747+4del is classified Uncertain significance in HTT (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-23). No gnomAD frequency available for this variant.

How common is HTT c.747+4del in the general population?

HTT c.747+4del is no gnomAD frequency available for this variant (gnomAD).

HTT c.747+4del

rs2110163447 · VCV1356024

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +4	donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.8	GERP -0.11, phastCons 1
Non-coding constraint	Z 0.41	1 kb window · o/e 0.97 · regional · uncalibrated

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: HTT
Coding: c.747+4del
MANE Select: NM_001388492
dbSNP: rs2110163447
Type: Deletion
Location: chr4:3107427 (GRCh38)
Structure: AlphaFold pLDDT 85.38 · 30 PDB

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

Similar variants

HTT c.5369-9del Likely benign ★★ same type
HTT p.Gln33fs Likely pathogenic ★ same type
HTT p.Gly697fs Pathogenic ★ same type
HTT p.Ser1941fs Pathogenic ★ same type
HTT c.2099-21_2099-13del Uncertain significance ★ same type
HTT c.7766-13_7766-8del Uncertain significance ★ same type
SLC6A4 c.*2091del Uncertain significance ★ same type
HTT c.264-17_264-14del Likely benign ★ 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/htt-c-747-plus-4del (accessed [today's date]).

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