chr3-47418189-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_012235.4(SCAP):c.2392G>A(p.Val798Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 1,574,632 control chromosomes in the GnomAD database, including 244,920 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_012235.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAP | NM_012235.4 | c.2392G>A | p.Val798Ile | missense_variant | 16/23 | ENST00000265565.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAP | ENST00000265565.10 | c.2392G>A | p.Val798Ile | missense_variant | 16/23 | 1 | NM_012235.4 | P1 | |
SCAP | ENST00000648151.1 | c.2392G>A | p.Val798Ile | missense_variant | 17/24 | P1 | |||
SCAP | ENST00000320017.10 | c.*1109G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/18 | 2 | ||||
SCAP | ENST00000441517.6 | c.*1541G>A | 3_prime_UTR_variant, NMD_transcript_variant | 13/20 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.478 AC: 72531AN: 151748Hom.: 18877 Cov.: 33
GnomAD3 exomes AF: 0.541 AC: 100584AN: 185836Hom.: 27854 AF XY: 0.546 AC XY: 54951AN XY: 100734
GnomAD4 exome AF: 0.560 AC: 797215AN: 1422766Hom.: 226035 Cov.: 66 AF XY: 0.560 AC XY: 394341AN XY: 704324
GnomAD4 genome ? AF: 0.478 AC: 72564AN: 151866Hom.: 18885 Cov.: 33 AF XY: 0.478 AC XY: 35505AN XY: 74226
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at