ENST00000377861.4:c.*10401_*10406delATATAT

Variant names:

• chr13-67214935-GATATAT-G
• rs66460017
• ENST00000377861.4:c.*10401_*10406delATATAT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000377861.4(PCDH9):​c.*10401_*10406delATATAT 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 0.0095 (44 hom., cov: 0)
• Consequence: PCDH9 ENST00000377861.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719
• 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.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0095 (848/89262) while in subpopulation AFR AF = 0.0288 (648/22482). AF 95% confidence interval is 0.027. There are 44 homozygotes in GnomAd4. There are 405 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High AC in GnomAd4 at 848 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377861.4. 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+10464_3036+10469delATATAT		intron	N/A	NP_982354.1	X5D7N0
	PCDH9	NM_001318374.2		c.*10401_*10406delATATAT		3_prime_UTR	Exon 2 of 2	NP_001305303.1	Q5VT82
	PCDH9	NM_020403.5		c.3036+10464_3036+10469delATATAT		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.*10401_*10406delATATAT		3_prime_UTR	Exon 2 of 2	ENSP00000367092.3	Q5VT82
	PCDH9	ENST00000377865.7	TSL:1 MANE Select	c.3036+10464_3036+10469delATATAT		intron	N/A	ENSP00000367096.2	Q9HC56-1
	PCDH9	ENST00000544246.5	TSL:1	c.3036+10464_3036+10469delATATAT		intron	N/A	ENSP00000442186.2	Q9HC56-2

Frequencies

GnomAD3 genomes AF: 0.00949 AC: 847 AN: 89220 Hom.: 44 Cov.: 0

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00330

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00810

Gnomad SAS AF: 0.00806

Gnomad FIN AF: 0.00108

Gnomad MID AF: 0.0122

Gnomad NFE AF: 0.00239

Gnomad OTH AF: 0.0121

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

GnomAD4 genome AF: 0.00950 AC: 848 AN: 89262 Hom.: 44 Cov.: 0 AF XY: 0.00944 AC XY: 405 AN XY: 42896

African (AFR) AF: 0.0288 AC: 648 AN: 22482

American (AMR) AF: 0.00329 AC: 27 AN: 8208

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2484

East Asian (EAS) AF: 0.00812 AC: 25 AN: 3080

South Asian (SAS) AF: 0.00806 AC: 25 AN: 3100

European-Finnish (FIN) AF: 0.00108 AC: 6 AN: 5562

Middle Eastern (MID) AF: 0.0130 AC: 2 AN: 154

European-Non Finnish (NFE) AF: 0.00239 AC: 101 AN: 42334

Other (OTH) AF: 0.0120 AC: 14 AN: 1164

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs66460017; hg19: chr13-67789067;