chr10-53807071-A-AGTT
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM4_SupportingPP3BP6_Very_StrongBA1
The NM_001384140.1(PCDH15):c.4728_4730dupAAC(p.Thr1577dup) variant causes a disruptive inframe insertion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00428 in 1,613,496 control chromosomes in the GnomAD database, including 226 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001384140.1 disruptive_inframe_insertion
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCDH15 | NM_001384140.1 | c.4728_4730dupAAC | p.Thr1577dup | disruptive_inframe_insertion | Exon 38 of 38 | ENST00000644397.2 | NP_001371069.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000644397.2 | c.4728_4730dupAAC | p.Thr1577dup | disruptive_inframe_insertion | Exon 38 of 38 | NM_001384140.1 | ENSP00000495195.1 |
Frequencies
GnomAD3 genomes AF: 0.0210 AC: 3196AN: 152122Hom.: 115 Cov.: 32
GnomAD3 exomes AF: 0.00551 AC: 1365AN: 247692Hom.: 42 AF XY: 0.00412 AC XY: 555AN XY: 134640
GnomAD4 exome AF: 0.00253 AC: 3700AN: 1461256Hom.: 111 Cov.: 32 AF XY: 0.00218 AC XY: 1585AN XY: 726892
GnomAD4 genome AF: 0.0211 AC: 3206AN: 152240Hom.: 115 Cov.: 32 AF XY: 0.0203 AC XY: 1510AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
p.Thr1519dup in exon 36C of PCDH15: This variant is not expected to have clinica l significance because it has been identified in 7.3% (707/9652) of African chro mosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.or g; dbSNP rs143978284). This variant is an insertion of 1 amino acid at position 1519 and is not predicted to alter the protein reading-frame. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at