4-3187820-C-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_001388492.1(HTT):c.5159C>A(p.Thr1720Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,611,318 control chromosomes in the GnomAD database, including 16,012 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1720S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001388492.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTT | NM_001388492.1 | c.5159C>A | p.Thr1720Asn | missense_variant | 39/67 | ENST00000355072.11 | |
HTT | NM_002111.8 | c.5165C>A | p.Thr1722Asn | missense_variant | 39/67 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTT | ENST00000355072.11 | c.5159C>A | p.Thr1720Asn | missense_variant | 39/67 | 1 | NM_001388492.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.194 AC: 29494AN: 151990Hom.: 4408 Cov.: 32
GnomAD3 exomes AF: 0.119 AC: 29785AN: 249434Hom.: 2767 AF XY: 0.117 AC XY: 15832AN XY: 135332
GnomAD4 exome AF: 0.111 AC: 162432AN: 1459210Hom.: 11579 Cov.: 30 AF XY: 0.110 AC XY: 80088AN XY: 726110
GnomAD4 genome AF: 0.194 AC: 29560AN: 152108Hom.: 4433 Cov.: 32 AF XY: 0.190 AC XY: 14150AN XY: 74346
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at