rs10492477

Positions:

• chr13-66767605-A-T

Variant summary

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

The NM_203487.3(PCDH9):​c.3138+135899T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0813 in 152,066 control chromosomes in the GnomAD database, including 524 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 0.081 (524 hom., cov: 32)
• Consequence: PCDH9 NM_203487.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492

Genes affected

PCDH9 (HGNC:8661): (protocadherin 9) This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCDH9	NM_203487.3	c.3138+135899T>A		intron_variant		ENST00000377865.7	NP_982354.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCDH9	ENST00000377865.7	c.3138+135899T>A		intron_variant		1	NM_203487.3	ENSP00000367096
PCDH9	ENST00000456367.5	c.3138+135899T>A		intron_variant		1		ENSP00000401699
PCDH9	ENST00000544246.5	c.3037-136194T>A		intron_variant		1		ENSP00000442186	P1
PCDH9	ENST00000614931.1	c.*51+15109T>A		intron_variant, NMD_transcript_variant		1		ENSP00000482917

Frequencies

GnomAD3 genomes AF: 0.0814 AC: 12362 AN: 151948 Hom.: 523 Cov.: 32

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0565

Gnomad ASJ AF: 0.0730

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0752

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.0882

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

GnomAD4 genome AF: 0.0813 AC: 12363 AN: 152066 Hom.: 524 Cov.: 32 AF XY: 0.0818 AC XY: 6080 AN XY: 74340

Gnomad4 AFR AF: 0.0752

Gnomad4 AMR AF: 0.0564

Gnomad4 ASJ AF: 0.0730

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.0755

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.0886

Gnomad4 OTH AF: 0.0873

Alfa AF: 0.0881 Hom.: 72

Bravo AF: 0.0789

Asia WGS AF: 0.121 AC: 423 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	16
DANN	Benign	0.91

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

Other links and lift over

dbSNP: rs10492477; hg19: chr13-67341737; COSMIC: COSV60584925;