chr3-47414632-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_012235.4(SCAP):c.3327G>A(p.Ser1109=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,218 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 (★). Synonymous variant affecting the same amino acid position (i.e. S1109S) has been classified as Benign.
Frequency
Consequence
NM_012235.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.3327G>A | p.Ser1109= | synonymous_variant | 21/23 | ENST00000265565.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAP | ENST00000265565.10 | c.3327G>A | p.Ser1109= | synonymous_variant | 21/23 | 1 | NM_012235.4 | P1 | |
SCAP | ENST00000648151.1 | c.3327G>A | p.Ser1109= | synonymous_variant | 22/24 | P1 | |||
SCAP | ENST00000320017.10 | c.*2041G>A | 3_prime_UTR_variant, NMD_transcript_variant | 16/18 | 2 | ||||
SCAP | ENST00000441517.6 | c.*2473G>A | 3_prime_UTR_variant, NMD_transcript_variant | 18/20 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250748Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135708
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460990Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726776
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | SCAP: BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at