ENST00000377861:c.*10379_*10406dupATATATATATATATATATATATATATAT

Variant names:

• chr13-67214935-G-GATATATATATATATATATATATATATAT
• rs66460017
• ENST00000377861.4:c.*10379_*10406dupATATATATATATATATATATATATATAT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000377861.4(PCDH9):​c.*10379_*10406dupATATATATATATATATATATATATATAT 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 INS_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 0.00071 (19 hom., cov: 0)
• Consequence: PCDH9 ENST00000377861.4 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 63 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+10442_3036+10469dupATATATATATATATATATATATATATAT		intron	N/A	NP_982354.1	X5D7N0
	PCDH9	NM_001318374.2		c.*10379_*10406dupATATATATATATATATATATATATATAT		3_prime_UTR	Exon 2 of 2	NP_001305303.1	Q5VT82
	PCDH9	NM_020403.5		c.3036+10442_3036+10469dupATATATATATATATATATATATATATAT		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.*10379_*10406dupATATATATATATATATATATATATATAT		3_prime_UTR	Exon 2 of 2	ENSP00000367092.3	Q5VT82
	PCDH9	ENST00000377865.7	TSL:1 MANE Select	c.3036+10442_3036+10469dupATATATATATATATATATATATATATAT		intron	N/A	ENSP00000367096.2	Q9HC56-1
	PCDH9	ENST00000544246.5	TSL:1	c.3036+10442_3036+10469dupATATATATATATATATATATATATATAT		intron	N/A	ENSP00000442186.2	Q9HC56-2

Frequencies

GnomAD3 genomes AF: 0.000740 AC: 66 AN: 89230 Hom.: 20 Cov.: 0

Gnomad AFR AF: 0.000445

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000488

Gnomad ASJ AF: 0.00161

Gnomad EAS AF: 0.00130

Gnomad SAS AF: 0.000323

Gnomad FIN AF: 0.000719

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000898

Gnomad OTH AF: 0.000867

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.000706 AC: 63 AN: 89272 Hom.: 19 Cov.: 0 AF XY: 0.000536 AC XY: 23 AN XY: 42896

African (AFR) AF: 0.000355 AC: 8 AN: 22506

American (AMR) AF: 0.000488 AC: 4 AN: 8204

Ashkenazi Jewish (ASJ) AF: 0.00161 AC: 4 AN: 2482

East Asian (EAS) AF: 0.00130 AC: 4 AN: 3076

South Asian (SAS) AF: 0.000323 AC: 1 AN: 3100

European-Finnish (FIN) AF: 0.000719 AC: 4 AN: 5560

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 154

European-Non Finnish (NFE) AF: 0.000874 AC: 37 AN: 42332

Other (OTH) AF: 0.000859 AC: 1 AN: 1164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.11

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;