rs1209403984
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001372044.2(SHANK3):c.2695G>A(p.Ala899Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 9/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A899P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001372044.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHANK3 | NM_001372044.2 | c.2695G>A | p.Ala899Thr | missense_variant | Exon 24 of 25 | NP_001358973.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHANK3 | ENST00000262795.7 | c.2110G>A | p.Ala704Thr | missense_variant | Exon 20 of 22 | 5 | ENSP00000489147.3 | |||
SHANK3 | ENST00000445220.7 | c.1162G>A | p.Ala388Thr | missense_variant | Exon 11 of 13 | 5 | ||||
SHANK3 | ENST00000664402.2 | c.652G>A | p.Ala218Thr | missense_variant | Exon 5 of 7 | ENSP00000499475.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1135934Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 556954
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at