13-67214935-GATATATATATATATATATATATATATATAT-GATATATATATATATATATATATATATATATATATAT

Variant names:

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

Variant summary

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

The NM_001318374.2(PCDH9):​c.*10401_*10406dupATATAT 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 0.031 (561 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 = 0.0311 (2769/88904) while in subpopulation NFE AF= 0.037 (1564/42236). AF 95% confidence interval is 0.0355. There are 561 homozygotes in gnomad4. There are 1268 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 2769 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH9	NM_203487.3	c.3036+10464_3036+10469dupATATAT		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.*10401_*10406dupATATAT		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000367092.3
PCDH9	ENST00000377865.7	c.3036+10464_3036+10469dupATATAT		intron_variant	Intron 2 of 4	1	NM_203487.3	ENSP00000367096.2
PCDH9	ENST00000544246.5	c.3036+10464_3036+10469dupATATAT		intron_variant	Intron 2 of 3	1		ENSP00000442186.2
PCDH9	ENST00000456367.5	c.3036+10464_3036+10469dupATATAT		intron_variant	Intron 2 of 4	1		ENSP00000401699.2

Frequencies

GnomAD3 genomes AF: 0.0312 AC: 2769 AN: 88862 Hom.: 561 Cov.: 0

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.0303

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0286

Gnomad EAS AF: 0.00910

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0183

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0279

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0311 AC: 2769 AN: 88904 Hom.: 561 Cov.: 0 AF XY: 0.0297 AC XY: 1268 AN XY: 42698

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0286

Gnomad4 EAS AF: 0.00911

Gnomad4 SAS AF: 0.0178

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.0370

Gnomad4 OTH AF: 0.0276

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;