chr20-1312498-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_080489.5(SDCBP2):c.571C>T(p.Arg191Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000139 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R191Q) has been classified as Likely benign.
Frequency
Consequence
NM_080489.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDCBP2 | NM_080489.5 | c.571C>T | p.Arg191Trp | missense_variant | 7/9 | ENST00000360779.4 | |
FKBP1A-SDCBP2 | NR_037661.1 | n.849C>T | non_coding_transcript_exon_variant | 8/10 | |||
SDCBP2 | NM_001199784.2 | c.571C>T | p.Arg191Trp | missense_variant | 7/9 | ||
SDCBP2 | NM_015685.6 | c.316C>T | p.Arg106Trp | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDCBP2 | ENST00000360779.4 | c.571C>T | p.Arg191Trp | missense_variant | 7/9 | 1 | NM_080489.5 | P1 | |
SDCBP2 | ENST00000339987.7 | c.571C>T | p.Arg191Trp | missense_variant | 7/9 | 1 | P1 | ||
SDCBP2 | ENST00000381808.7 | c.316C>T | p.Arg106Trp | missense_variant | 3/5 | 1 | |||
SDCBP2 | ENST00000381812.5 | c.571C>T | p.Arg191Trp | missense_variant | 7/9 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251084Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135764
GnomAD4 exome AF: 0.000137 AC: 200AN: 1461806Hom.: 0 Cov.: 63 AF XY: 0.000124 AC XY: 90AN XY: 727210
GnomAD4 genome AF: 0.000158 AC: 24AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2023 | The c.571C>T (p.R191W) alteration is located in exon 7 (coding exon 6) of the SDCBP2 gene. This alteration results from a C to T substitution at nucleotide position 571, causing the arginine (R) at amino acid position 191 to be replaced by a tryptophan (W). 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