ENST00000377861:c.*10385_*10406dupATATATATATATATATATATAT

Variant names:

• chr13-67214935-G-GATATATATATATATATATATAT
• rs66460017
• ENST00000377861.4:c.*10385_*10406dupATATATATATATATATATATAT

Variant summary

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

The ENST00000377861.4(PCDH9):​c.*10385_*10406dupATATATATATATATATATATAT 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 0.0080 (202 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 712 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+10448_3036+10469dupATATATATATATATATATATAT		intron	N/A	NP_982354.1	X5D7N0
	PCDH9	NM_001318374.2		c.*10385_*10406dupATATATATATATATATATATAT		3_prime_UTR	Exon 2 of 2	NP_001305303.1	Q5VT82
	PCDH9	NM_020403.5		c.3036+10448_3036+10469dupATATATATATATATATATATAT		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.*10385_*10406dupATATATATATATATATATATAT		3_prime_UTR	Exon 2 of 2	ENSP00000367092.3	Q5VT82
	PCDH9	ENST00000377865.7	TSL:1 MANE Select	c.3036+10448_3036+10469dupATATATATATATATATATATAT		intron	N/A	ENSP00000367096.2	Q9HC56-1
	PCDH9	ENST00000544246.5	TSL:1	c.3036+10448_3036+10469dupATATATATATATATATATATAT		intron	N/A	ENSP00000442186.2	Q9HC56-2

Frequencies

GnomAD3 genomes AF: 0.00800 AC: 713 AN: 89138 Hom.: 203 Cov.: 0

Gnomad AFR AF: 0.00383

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00575

Gnomad ASJ AF: 0.0117

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.00453

Gnomad FIN AF: 0.00108

Gnomad MID AF: 0.0366

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.00781

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00798 AC: 712 AN: 89180 Hom.: 202 Cov.: 0 AF XY: 0.00703 AC XY: 301 AN XY: 42832

African (AFR) AF: 0.00387 AC: 87 AN: 22486

American (AMR) AF: 0.00574 AC: 47 AN: 8184

Ashkenazi Jewish (ASJ) AF: 0.0117 AC: 29 AN: 2482

East Asian (EAS) AF: 0.0124 AC: 38 AN: 3076

South Asian (SAS) AF: 0.00485 AC: 15 AN: 3090

European-Finnish (FIN) AF: 0.00108 AC: 6 AN: 5556

Middle Eastern (MID) AF: 0.0195 AC: 3 AN: 154

European-Non Finnish (NFE) AF: 0.0113 AC: 478 AN: 42296

Other (OTH) AF: 0.00775 AC: 9 AN: 1162

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;