rs1249328324
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020777.3(SORCS2):c.46A>C(p.Thr16Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000405 in 987,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign 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. T16S) has been classified as Uncertain significance.
Frequency
Consequence
NM_020777.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000689 AC: 1AN: 145158Hom.: 0 Cov.: 32 show subpopulations
GnomAD4 exome AF: 0.00000356 AC: 3AN: 842456Hom.: 0 Cov.: 29 AF XY: 0.00000769 AC XY: 3AN XY: 390026 show subpopulations
GnomAD4 genome AF: 0.00000689 AC: 1AN: 145158Hom.: 0 Cov.: 32 AF XY: 0.0000142 AC XY: 1AN XY: 70604 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.46A>C (p.T16P) alteration is located in exon 1 (coding exon 1) of the SORCS2 gene. This alteration results from a A to C substitution at nucleotide position 46, causing the threonine (T) at amino acid position 16 to be replaced by a proline (P). 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