10-55089031-T-C

Position:

• chr10-55089031-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001354404.2(PCDH15):​c.-80+77545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 152,214 control chromosomes in the GnomAD database, including 302 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 0.041 (302 hom., cov: 32)
• Consequence: PCDH15 NM_001354404.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCDH15	NM_001354404.2	c.-80+77545A>G		intron_variant			NP_001341333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCDH15	ENST00000458638.1	c.-80+77545A>G		intron_variant		5		ENSP00000394465
PCDH15	ENST00000613346.4	c.-80+77545A>G		intron_variant		4		ENSP00000481211

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6137 AN: 152096 Hom.: 292 Cov.: 32

Gnomad AFR AF: 0.0525

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0553

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.00395

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0473

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0405 AC: 6172 AN: 152214 Hom.: 302 Cov.: 32 AF XY: 0.0424 AC XY: 3153 AN XY: 74408

Gnomad4 AFR AF: 0.0529

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0553

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0321

Gnomad4 FIN AF: 0.00395

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0487

Alfa AF: 0.0200 Hom.: 18

Bravo AF: 0.0507

Asia WGS AF: 0.0990 AC: 342 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10509021; hg19: chr10-56848791;