Is HTT p.Asn2499= (c.7497C>T) pathogenic?

HTT p.Asn2499= (c.7497C>T) is classified Benign/Likely benign in HTT (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-25). Ultra-rare (popmax 0.048%, nfe).

How common is HTT p.Asn2499= (c.7497C>T) in the general population?

HTT p.Asn2499= (c.7497C>T) is ultra-rare (popmax 0.048%, nfe) (gnomAD).

HTT p.Asn2499=

c.7497C>T · rs190850312 · VCV1539804

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.048%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -7	GERP -3.9
Overall
CADD	0.808	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.048% European (non-Finnish) · 564/1,174,604 alleles

Filtering AF 0.0447% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0434%

Overall 0.0663% 1,063/1,603,168 alleles · ultra-rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.682%	147
Remaining individualsnot grpmax-eligible	0.055%	1,819
European (non-Finnish)grpmax	0.048%	2,083
African / African-American	0.0214%	4,668
Middle Eastern	0.0166%	6,030
Admixed American	0.0104%	9,642
South Asian	0.00557%	17,939
Ashkenazi Jewishnot grpmax-eligible	0.00342%	29,242

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: HTT
Protein: p.Asn2499=
Coding: c.7497C>T
MANE Select: NM_001045 · reported on NM_001388492
dbSNP: rs190850312
Type: single nucleotide variant
Location: chr4:3223432 (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.889+6G>T Uncertain significance ★★ same type
HTT p.Ala2739Thr Uncertain significance ★★ same type
HTT p.Arg1654Trp Uncertain significance ★★ same type
HTT p.Arg1945Trp Uncertain significance ★★ same type
HTT p.Asp1157Gly Uncertain significance ★★ same type
HTT p.Asp920Asn Uncertain significance ★★ same type
HTT p.Glu449Ala Uncertain significance ★★ ⚠ same type
HTT p.Gly2084Arg 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/htt-p-asn2499 (accessed [today's date]).

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