chr1-87073006-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_012262.4(HS2ST1):c.197C>T(p.Ala66Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,613,996 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_012262.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HS2ST1 | NM_012262.4 | c.197C>T | p.Ala66Val | missense_variant | 2/7 | ENST00000370550.10 | |
HS2ST1 | NM_001134492.2 | c.197C>T | p.Ala66Val | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HS2ST1 | ENST00000370550.10 | c.197C>T | p.Ala66Val | missense_variant | 2/7 | 1 | NM_012262.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000631 AC: 96AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000183 AC: 46AN: 251010Hom.: 1 AF XY: 0.000177 AC XY: 24AN XY: 135664
GnomAD4 exome AF: 0.0000629 AC: 92AN: 1461688Hom.: 1 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727146
GnomAD4 genome ? AF: 0.000630 AC: 96AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000685 AC XY: 51AN XY: 74476
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
HS2ST1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 10, 2023 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at