NM_033056.4:c.1306-4123C>T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_033056.4(PCDH15):c.1306-4123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,522,380 control chromosomes in the GnomAD database, including 36,148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_033056.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDH15 | ENST00000320301.11 | c.1306-4123C>T | intron_variant | Intron 11 of 32 | 1 | NM_033056.4 | ENSP00000322604.6 | |||
PCDH15 | ENST00000644397.2 | c.1306-4123C>T | intron_variant | Intron 11 of 37 | NM_001384140.1 | ENSP00000495195.1 |
Frequencies
GnomAD3 genomes AF: 0.175 AC: 26488AN: 151684Hom.: 3756 Cov.: 32
GnomAD3 exomes AF: 0.235 AC: 40068AN: 170490Hom.: 7697 AF XY: 0.237 AC XY: 21573AN XY: 91120
GnomAD4 exome AF: 0.172 AC: 235065AN: 1370578Hom.: 32391 Cov.: 27 AF XY: 0.176 AC XY: 119500AN XY: 678250
GnomAD4 genome AF: 0.175 AC: 26498AN: 151802Hom.: 3757 Cov.: 32 AF XY: 0.185 AC XY: 13707AN XY: 74180
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
1321-7C>T in Intron 12 of PCDH15: This variant is not expected to have clinical significance because it has been identified in 12.6% (685/5434) of European Amer ican chromosomes from a broad population by the NHLBI Exome Sequencing Project ( http://evs.gs.washington.edu/EVS; dbSNP rs16905686). -
Usher syndrome type 1F Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at