chr3-47414586-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012235.4(SCAP):c.3373G>A(p.Val1125Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00029 in 1,613,462 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012235.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAP | NM_012235.4 | c.3373G>A | p.Val1125Met | missense_variant | 21/23 | ENST00000265565.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAP | ENST00000265565.10 | c.3373G>A | p.Val1125Met | missense_variant | 21/23 | 1 | NM_012235.4 | P1 | |
SCAP | ENST00000648151.1 | c.3373G>A | p.Val1125Met | missense_variant | 22/24 | P1 | |||
SCAP | ENST00000320017.10 | c.*2087G>A | 3_prime_UTR_variant, NMD_transcript_variant | 16/18 | 2 | ||||
SCAP | ENST00000441517.6 | c.*2519G>A | 3_prime_UTR_variant, NMD_transcript_variant | 18/20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000355 AC: 89AN: 250814Hom.: 0 AF XY: 0.000332 AC XY: 45AN XY: 135746
GnomAD4 exome AF: 0.000292 AC: 426AN: 1461114Hom.: 0 Cov.: 32 AF XY: 0.000268 AC XY: 195AN XY: 726862
GnomAD4 genome AF: 0.000276 AC: 42AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 31, 2022 | The c.3373G>A (p.V1125M) alteration is located in exon 21 (coding exon 20) of the SCAP gene. This alteration results from a G to A substitution at nucleotide position 3373, causing the valine (V) at amino acid position 1125 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at