ENST00000377861.4:c.*10381_*10406delATATATATATATATATATATATATAT

Variant names:

• chr13-67214935-GATATATATATATATATATATATATAT-G
• rs66460017
• ENST00000377861.4:c.*10381_*10406delATATATATATATATATATATATATAT

Variant summary

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

The ENST00000377861.4(PCDH9):​c.*10381_*10406delATATATATATATATATATATATATAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.39 (7246 hom., cov: 0)
  • Failed GnomAD Quality Control
• 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.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

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+10444_3036+10469delATATATATATATATATATATATATAT		intron	N/A	NP_982354.1	X5D7N0
	PCDH9	NM_001318374.2		c.*10381_*10406delATATATATATATATATATATATATAT		3_prime_UTR	Exon 2 of 2	NP_001305303.1	Q5VT82
	PCDH9	NM_020403.5		c.3036+10444_3036+10469delATATATATATATATATATATATATAT		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.*10381_*10406delATATATATATATATATATATATATAT		3_prime_UTR	Exon 2 of 2	ENSP00000367092.3	Q5VT82
	PCDH9	ENST00000377865.7	TSL:1 MANE Select	c.3036+10444_3036+10469delATATATATATATATATATATATATAT		intron	N/A	ENSP00000367096.2	Q9HC56-1
	PCDH9	ENST00000544246.5	TSL:1	c.3036+10444_3036+10469delATATATATATATATATATATATATAT		intron	N/A	ENSP00000442186.2	Q9HC56-2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 34686 AN: 89402 Hom.: 7227 Cov.: 0

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.388 AC: 34727 AN: 89444 Hom.: 7246 Cov.: 0 AF XY: 0.412 AC XY: 17728 AN XY: 42996

African (AFR) AF: 0.301 AC: 6789 AN: 22558

American (AMR) AF: 0.503 AC: 4146 AN: 8236

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1065 AN: 2484

East Asian (EAS) AF: 0.508 AC: 1567 AN: 3082

South Asian (SAS) AF: 0.506 AC: 1572 AN: 3104

European-Finnish (FIN) AF: 0.651 AC: 3636 AN: 5582

Middle Eastern (MID) AF: 0.397 AC: 62 AN: 156

European-Non Finnish (NFE) AF: 0.357 AC: 15127 AN: 42384

Other (OTH) AF: 0.388 AC: 452 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
Mutation Taster		=100/0	polymorphism (auto)

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;