chr11-70473146-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_012309.5(SHANK2):c.5273C>T(p.Ala1758Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,100 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A1758A) has been classified as Likely benign.
Frequency
Consequence
NM_012309.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHANK2 | NM_012309.5 | c.5273C>T | p.Ala1758Val | missense_variant | 26/26 | ENST00000601538.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHANK2 | ENST00000601538.6 | c.5273C>T | p.Ala1758Val | missense_variant | 26/26 | 5 | NM_012309.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251436Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135902
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461884Hom.: 1 Cov.: 32 AF XY: 0.0000660 AC XY: 48AN XY: 727244
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74354
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | SHANK2: BP4 - |
Uncertain significance, no assertion criteria provided | clinical testing | Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare | Apr 08, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at