chr4-7192683-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_020777.3(SORCS2):c.37C>T(p.Pro13Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 988,626 control chromosomes in the GnomAD database, including 3 homozygotes. 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_020777.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SORCS2 | NM_020777.3 | c.37C>T | p.Pro13Ser | missense_variant | 1/27 | ENST00000507866.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SORCS2 | ENST00000507866.6 | c.37C>T | p.Pro13Ser | missense_variant | 1/27 | 1 | NM_020777.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000954 AC: 140AN: 146676Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00169 AC: 1424AN: 841844Hom.: 3 Cov.: 30 AF XY: 0.00170 AC XY: 664AN XY: 389710
GnomAD4 genome ? AF: 0.000954 AC: 140AN: 146782Hom.: 0 Cov.: 32 AF XY: 0.000686 AC XY: 49AN XY: 71476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.37C>T (p.P13S) alteration is located in exon 1 (coding exon 1) of the SORCS2 gene. This alteration results from a C to T substitution at nucleotide position 37, causing the proline (P) at amino acid position 13 to be replaced by a serine (S). 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