13-67214935-GATATATATATATATATATATATATATATAT-GATATATATATATATATATATATATATATATATATATATATATATATATAT

Variant names:

• chr13-67214935-G-GATATATATATATATATATAT
• rs66460017
• ENST00000377861:c.*10387_*10406dupATATATATATATATATATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001318374.2(PCDH9):​c.*10387_*10406dupATATATATATATATATATAT 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 0.021 (576 hom., cov: 0)
• Consequence: PCDH9 NM_001318374.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114

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

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0214 (1904/89062) while in subpopulation NFE AF= 0.0292 (1232/42228). AF 95% confidence interval is 0.0278. There are 576 homozygotes in gnomad4. There are 840 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1904 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH9	NM_203487.3	c.3036+10450_3036+10469dupATATATATATATATATATAT		intron_variant	Intron 2 of 4	ENST00000377865.7	NP_982354.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCDH9	ENST00000377861	c.*10387_*10406dupATATATATATATATATATAT		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000367092.3
PCDH9	ENST00000377865.7	c.3036+10450_3036+10469dupATATATATATATATATATAT		intron_variant	Intron 2 of 4	1	NM_203487.3	ENSP00000367096.2
PCDH9	ENST00000544246.5	c.3036+10450_3036+10469dupATATATATATATATATATAT		intron_variant	Intron 2 of 3	1		ENSP00000442186.2
PCDH9	ENST00000456367.5	c.3036+10450_3036+10469dupATATATATATATATATATAT		intron_variant	Intron 2 of 4	1		ENSP00000401699.2

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 1907 AN: 89020 Hom.: 577 Cov.: 0

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.00434

Gnomad AMR AF: 0.0163

Gnomad ASJ AF: 0.0391

Gnomad EAS AF: 0.0182

Gnomad SAS AF: 0.0181

Gnomad FIN AF: 0.00487

Gnomad MID AF: 0.0427

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0252

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0214 AC: 1904 AN: 89062 Hom.: 576 Cov.: 0 AF XY: 0.0196 AC XY: 840 AN XY: 42782

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0164

Gnomad4 ASJ AF: 0.0391

Gnomad4 EAS AF: 0.0182

Gnomad4 SAS AF: 0.0175

Gnomad4 FIN AF: 0.00487

Gnomad4 NFE AF: 0.0292

Gnomad4 OTH AF: 0.0250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs66460017; hg19: chr13-67789067;