15-76381446-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_020843.4(SCAPER):c.3637A>G(p.Ile1213Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,804 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 (★). Synonymous variant affecting the same amino acid position (i.e. I1213I) has been classified as Benign.
Frequency
Consequence
NM_020843.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAPER | NM_020843.4 | c.3637A>G | p.Ile1213Val | missense_variant | 28/32 | ENST00000563290.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAPER | ENST00000563290.6 | c.3637A>G | p.Ile1213Val | missense_variant | 28/32 | 5 | NM_020843.4 | P1 | |
SCAPER | ENST00000324767.11 | c.3637A>G | p.Ile1213Val | missense_variant | 27/31 | 1 | P1 | ||
SCAPER | ENST00000538941.6 | c.2899A>G | p.Ile967Val | missense_variant | 28/32 | 1 | |||
SCAPER | ENST00000303521.10 | n.3701A>G | non_coding_transcript_exon_variant | 27/27 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248880Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134988
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461590Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727066
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74416
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | 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