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rs1937395

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033056.4(PCDH15):c.91+32629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,900 control chromosomes in the GnomAD database, including 3,250 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3250 hom., cov: 32)

Consequence

PCDH15
NM_033056.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.716
Variant links:
Genes affected
PCDH15 (HGNC:14674): (protocadherin related 15) This gene is a member of the cadherin superfamily. Family members encode integral membrane proteins that mediate calcium-dependent cell-cell adhesion. It plays an essential role in maintenance of normal retinal and cochlear function. Mutations in this gene result in hearing loss and Usher Syndrome Type IF (USH1F). Extensive alternative splicing resulting in multiple isoforms has been observed in the mouse ortholog. Similar alternatively spliced transcripts are inferred to occur in human, and additional variants are likely to occur. [provided by RefSeq, Dec 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PCDH15NM_001384140.1 linkuse as main transcriptc.91+32629C>T intron_variant ENST00000644397.2
PCDH15NM_033056.4 linkuse as main transcriptc.91+32629C>T intron_variant ENST00000320301.11
LOC105378311NR_134503.1 linkuse as main transcriptn.1683+12219G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PCDH15ENST00000320301.11 linkuse as main transcriptc.91+32629C>T intron_variant 1 NM_033056.4 Q96QU1-1
PCDH15ENST00000644397.2 linkuse as main transcriptc.91+32629C>T intron_variant NM_001384140.1
ENST00000422842.1 linkuse as main transcriptn.1683+12219G>A intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.199
AC:
30133
AN:
151782
Hom.:
3248
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.128
Gnomad AMI
AF:
0.156
Gnomad AMR
AF:
0.248
Gnomad ASJ
AF:
0.138
Gnomad EAS
AF:
0.395
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.207
Gnomad MID
AF:
0.143
Gnomad NFE
AF:
0.215
Gnomad OTH
AF:
0.215
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.198
AC:
30135
AN:
151900
Hom.:
3250
Cov.:
32
AF XY:
0.201
AC XY:
14899
AN XY:
74220
show subpopulations
Gnomad4 AFR
AF:
0.128
Gnomad4 AMR
AF:
0.248
Gnomad4 ASJ
AF:
0.138
Gnomad4 EAS
AF:
0.394
Gnomad4 SAS
AF:
0.232
Gnomad4 FIN
AF:
0.207
Gnomad4 NFE
AF:
0.215
Gnomad4 OTH
AF:
0.218
Alfa
AF:
0.207
Hom.:
2965
Bravo
AF:
0.200
Asia WGS
AF:
0.313
AC:
1087
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
1.3
Dann
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1937395; hg19: chr10-56391303; API