NM_020777.3:c.79C>T
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_020777.3(SORCS2):c.79C>T(p.Pro27Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000911 in 990,754 control chromosomes in the GnomAD database, including 7 homozygotes. 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 (★).
Frequency
Consequence
NM_020777.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00393 AC: 575AN: 146384Hom.: 2 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00 AC: 0AN: 14 AF XY: 0.00
GnomAD4 exome AF: 0.000389 AC: 328AN: 844266Hom.: 5 Cov.: 29 AF XY: 0.000343 AC XY: 134AN XY: 391178 show subpopulations
GnomAD4 genome AF: 0.00393 AC: 575AN: 146488Hom.: 2 Cov.: 32 AF XY: 0.00377 AC XY: 269AN XY: 71326 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.79C>T (p.P27S) 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 79, causing the proline (P) at amino acid position 27 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