chr10-53995658-T-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_033056.4(PCDH15):āc.2859A>Cā(p.Ala953=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. A953A) has been classified as Likely benign.
Frequency
Consequence
NM_033056.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH15 | NM_033056.4 | c.2859A>C | p.Ala953= | synonymous_variant | 21/33 | ENST00000320301.11 | |
PCDH15 | NM_001384140.1 | c.2859A>C | p.Ala953= | synonymous_variant | 21/38 | ENST00000644397.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000320301.11 | c.2859A>C | p.Ala953= | synonymous_variant | 21/33 | 1 | NM_033056.4 | ||
PCDH15 | ENST00000644397.2 | c.2859A>C | p.Ala953= | synonymous_variant | 21/38 | NM_001384140.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461654Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727122
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 19, 2017 | p.Ala953Ala in Exon 21 of PCDH15: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 1/66716 European c hromosomes by the Exome Aggregation Consortium (http://exac.broadinstitute.org/; dbSNP rs375965861). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at