11-626517-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021920.4(SCT):c.280G>A(p.Gly94Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000628 in 1,559,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021920.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCT | NM_021920.4 | c.280G>A | p.Gly94Arg | missense_variant | 4/4 | ENST00000176195.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCT | ENST00000176195.4 | c.280G>A | p.Gly94Arg | missense_variant | 4/4 | 1 | NM_021920.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 8AN: 166658Hom.: 0 AF XY: 0.0000794 AC XY: 7AN XY: 88126
GnomAD4 exome AF: 0.0000633 AC: 89AN: 1407108Hom.: 0 Cov.: 32 AF XY: 0.0000748 AC XY: 52AN XY: 694738
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at