chr13-67214935-GAT-G

Variant names:

• chr13-67214935-GAT-G
• rs66460017
• ENST00000377861.4:c.*10405_*10406delAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001318374.2(PCDH9):​c.*10405_*10406delAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.068 (404 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: PCDH9 NM_001318374.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 0 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]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0844 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318374.2. 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+10468_3036+10469delAT		intron	N/A	NP_982354.1	X5D7N0
	PCDH9	NM_001318374.2		c.*10405_*10406delAT		3_prime_UTR	Exon 2 of 2	NP_001305303.1	Q5VT82
	PCDH9	NM_020403.5		c.3036+10468_3036+10469delAT		intron	N/A	NP_065136.1	Q9HC56-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDH9	ENST00000377861.4	TSL:1	c.*10405_*10406delAT		3_prime_UTR	Exon 2 of 2	ENSP00000367092.3	Q5VT82
	PCDH9	ENST00000377865.7	TSL:1 MANE Select	c.3036+10468_3036+10469delAT		intron	N/A	ENSP00000367096.2	Q9HC56-1
	PCDH9	ENST00000544246.5	TSL:1	c.3036+10468_3036+10469delAT		intron	N/A	ENSP00000442186.2	Q9HC56-2

Frequencies

GnomAD3 genomes AF: 0.0681 AC: 6008 AN: 88204 Hom.: 404 Cov.: 0

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0370

Gnomad NFE AF: 0.0867

Gnomad OTH AF: 0.0596

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

GnomAD4 genome AF: 0.0680 AC: 6005 AN: 88248 Hom.: 404 Cov.: 0 AF XY: 0.0652 AC XY: 2760 AN XY: 42348

African (AFR) AF: 0.0522 AC: 1168 AN: 22368

American (AMR) AF: 0.0448 AC: 365 AN: 8150

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 84 AN: 2472

East Asian (EAS) AF: 0.0396 AC: 121 AN: 3056

South Asian (SAS) AF: 0.0461 AC: 141 AN: 3060

European-Finnish (FIN) AF: 0.0528 AC: 288 AN: 5450

Middle Eastern (MID) AF: 0.0329 AC: 5 AN: 152

European-Non Finnish (NFE) AF: 0.0868 AC: 3620 AN: 41724

Other (OTH) AF: 0.0609 AC: 70 AN: 1150

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.11
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: rs66460017; hg19: chr13-67789067;