chr5-63961256-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000524.4(HTR1A):c.464C>G(p.Ala155Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000266 in 1,614,180 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A155A) has been classified as Likely benign.
Frequency
Consequence
NM_000524.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HTR1A | NM_000524.4 | c.464C>G | p.Ala155Gly | missense_variant | 1/1 | ENST00000323865.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HTR1A | ENST00000323865.5 | c.464C>G | p.Ala155Gly | missense_variant | 1/1 | NM_000524.4 | P1 | ||
ENST00000502882.1 | n.97-3241C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000681 AC: 170AN: 249472Hom.: 2 AF XY: 0.000571 AC XY: 77AN XY: 134934
GnomAD4 exome AF: 0.000267 AC: 391AN: 1461834Hom.: 2 Cov.: 31 AF XY: 0.000256 AC XY: 186AN XY: 727208
GnomAD4 genome ? AF: 0.000249 AC: 38AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.000268 AC XY: 20AN XY: 74502
ClinVar
Submissions by phenotype
HTR1A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 01, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at