chr5-149027871-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate
The NM_024577.4(SH3TC2):c.1861C>T(p.Arg621Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,613,864 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R621H) has been classified as Likely benign.
Frequency
Consequence
NM_024577.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3TC2 | NM_024577.4 | c.1861C>T | p.Arg621Cys | missense_variant | 11/17 | ENST00000515425.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3TC2 | ENST00000515425.6 | c.1861C>T | p.Arg621Cys | missense_variant | 11/17 | 1 | NM_024577.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000758 AC: 19AN: 250508Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135562
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461542Hom.: 0 Cov.: 33 AF XY: 0.0000578 AC XY: 42AN XY: 727100
GnomAD4 genome AF: 0.000105 AC: 16AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74480
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease type 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at