rs201302313
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004821.3(HAND1):c.247G>T(p.Gly83Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00171 in 1,607,860 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G83R) has been classified as Uncertain significance.
Frequency
Consequence
NM_004821.3 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 |
---|---|---|---|---|---|---|---|
HAND1 | NM_004821.3 | c.247G>T | p.Gly83Trp | missense_variant | 1/2 | ENST00000231121.3 | |
HAND1 | XM_005268531.2 | c.247G>T | p.Gly83Trp | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAND1 | ENST00000231121.3 | c.247G>T | p.Gly83Trp | missense_variant | 1/2 | 1 | NM_004821.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00170 AC: 258AN: 151574Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00145 AC: 337AN: 232082Hom.: 0 AF XY: 0.00152 AC XY: 194AN XY: 127364
GnomAD4 exome AF: 0.00171 AC: 2489AN: 1456170Hom.: 5 Cov.: 33 AF XY: 0.00170 AC XY: 1231AN XY: 724504
GnomAD4 genome ? AF: 0.00170 AC: 258AN: 151690Hom.: 0 Cov.: 32 AF XY: 0.00166 AC XY: 123AN XY: 74136
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Nov 10, 2015 | - - |
HAND1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 03, 2020 | 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). - |
Hypoplastic left heart syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at