10-104641718-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014978.3(SORCS3):āc.391A>Cā(p.Ser131Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,541,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014978.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SORCS3 | NM_014978.3 | c.391A>C | p.Ser131Arg | missense_variant | 1/27 | ENST00000369701.8 | NP_055793.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SORCS3 | ENST00000369701.8 | c.391A>C | p.Ser131Arg | missense_variant | 1/27 | 1 | NM_014978.3 | ENSP00000358715 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152006Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000679 AC: 9AN: 132528Hom.: 0 AF XY: 0.0000416 AC XY: 3AN XY: 72192
GnomAD4 exome AF: 0.000114 AC: 158AN: 1389656Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 83AN XY: 685288
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 24, 2024 | The c.391A>C (p.S131R) alteration is located in exon 1 (coding exon 1) of the SORCS3 gene. This alteration results from a A to C substitution at nucleotide position 391, causing the serine (S) at amino acid position 131 to be replaced by an arginine (R). 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