chr13-66626810-C-A

Variant names:

• chr13-66626810-C-A
• rs10492473
• NM_203487.3:c.3340+4400G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_203487.3(PCDH9):​c.3340+4400G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 152,148 control chromosomes in the GnomAD database, including 346 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 0.048 (346 hom., cov: 32)
• Consequence: PCDH9 NM_203487.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43
• Publications: 1 publications found

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]

LOC105370247 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH9	NM_203487.3	c.3340+4400G>T		intron_variant	Intron 4 of 4	ENST00000377865.7	NP_982354.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCDH9	ENST00000377865.7	c.3340+4400G>T		intron_variant	Intron 4 of 4	1	NM_203487.3	ENSP00000367096.2
PCDH9	ENST00000544246.5	c.3238+4400G>T		intron_variant	Intron 3 of 3	1		ENSP00000442186.2
PCDH9	ENST00000456367.5	c.3214+4400G>T		intron_variant	Intron 4 of 4	1		ENSP00000401699.2
PCDH9	ENST00000614931.1	n.*253+4400G>T		intron_variant	Intron 3 of 3	1		ENSP00000482917.1

Frequencies

GnomAD3 genomes AF: 0.0482 AC: 7326 AN: 152030 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.0170

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.0116

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0483 AC: 7353 AN: 152148 Hom.: 346 Cov.: 32 AF XY: 0.0474 AC XY: 3530 AN XY: 74400

African (AFR) AF: 0.122 AC: 5045 AN: 41498

American (AMR) AF: 0.0304 AC: 465 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0170 AC: 59 AN: 3472

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5172

South Asian (SAS) AF: 0.0322 AC: 155 AN: 4820

European-Finnish (FIN) AF: 0.0116 AC: 123 AN: 10590

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0181 AC: 1233 AN: 67996

Other (OTH) AF: 0.0468 AC: 99 AN: 2114

Alfa AF: 0.0314 Hom.: 246

Bravo AF: 0.0528

Asia WGS AF: 0.0420 AC: 145 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.042
DANN	Benign	0.61
PhyloP100		-3.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10492473; hg19: chr13-67200942;