13-67122013-G-A

Variant names:

• chr13-67122013-G-A
• rs2875517
• NM_203487.3:c.3036+103392C>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.3036+103392C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,244 control chromosomes in the GnomAD database, including 65,113 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 0.92 (65113 hom., cov: 31)
• Consequence: PCDH9 NM_203487.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 6 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]

ENSG00000285588 (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 (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_203487.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDH9	NM_203487.3	MANE Select	c.3036+103392C>T		intron	N/A	NP_982354.1	X5D7N0
	PCDH9	NM_020403.5		c.3036+103392C>T		intron	N/A	NP_065136.1	Q9HC56-2
	PCDH9	NM_001318372.2		c.3036+103392C>T		intron	N/A	NP_001305301.1	B7ZM79

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDH9	ENST00000377865.7	TSL:1 MANE Select	c.3036+103392C>T		intron	N/A	ENSP00000367096.2	Q9HC56-1
	PCDH9	ENST00000544246.5	TSL:1	c.3036+103392C>T		intron	N/A	ENSP00000442186.2	Q9HC56-2
	PCDH9	ENST00000456367.5	TSL:1	c.3036+103392C>T		intron	N/A	ENSP00000401699.2	B7ZM79

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140593 AN: 152126 Hom.: 65061 Cov.: 31

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.924 AC: 140703 AN: 152244 Hom.: 65113 Cov.: 31 AF XY: 0.925 AC XY: 68818 AN XY: 74428

African (AFR) AF: 0.878 AC: 36477 AN: 41540

American (AMR) AF: 0.939 AC: 14365 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3386 AN: 3470

East Asian (EAS) AF: 0.978 AC: 5049 AN: 5164

South Asian (SAS) AF: 0.953 AC: 4594 AN: 4822

European-Finnish (FIN) AF: 0.915 AC: 9722 AN: 10620

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63969 AN: 68016

Other (OTH) AF: 0.933 AC: 1972 AN: 2114

Alfa AF: 0.936 Hom.: 200035

Bravo AF: 0.924

Asia WGS AF: 0.930 AC: 3223 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.18
DANN	Benign	0.22
PhyloP100		-0.53
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: rs2875517; hg19: chr13-67696145;