NM_001372044.2:c.1989G>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001372044.2(SHANK3):c.1989G>A(p.Thr663Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000833 in 1,609,424 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001372044.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHANK3 | NM_001372044.2 | c.1989G>A | p.Thr663Thr | synonymous_variant | Exon 18 of 25 | NP_001358973.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHANK3 | ENST00000262795.7 | c.1404G>A | p.Thr468Thr | synonymous_variant | Exon 14 of 22 | 5 | ENSP00000489147.3 | |||
SHANK3 | ENST00000445220.7 | c.456G>A | p.Thr152Thr | synonymous_variant | Exon 5 of 13 | 5 | ||||
SHANK3 | ENST00000414786.7 | n.1988G>A | non_coding_transcript_exon_variant | Exon 15 of 23 | 5 | |||||
SHANK3 | ENST00000673971.2 | n.1761G>A | non_coding_transcript_exon_variant | Exon 15 of 23 | ENSP00000501192.2 |
Frequencies
GnomAD3 genomes AF: 0.00329 AC: 500AN: 152162Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000923 AC: 220AN: 238406Hom.: 0 AF XY: 0.000646 AC XY: 84AN XY: 130026
GnomAD4 exome AF: 0.000578 AC: 842AN: 1457144Hom.: 2 Cov.: 32 AF XY: 0.000558 AC XY: 404AN XY: 724518
GnomAD4 genome AF: 0.00328 AC: 499AN: 152280Hom.: 1 Cov.: 32 AF XY: 0.00303 AC XY: 226AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:4
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SHANK3: BP4, BP7, BS1 -
not specified Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at