13-67214935-GATATATATATATATATATATATATATATAT-GATATATATATATATATATATATATATATATATATATATATAT

Variant names:

• chr13-67214935-G-GATATATATATAT
• rs66460017
• ENST00000377861:c.*10395_*10406dupATATATATATAT

Variant summary

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

The NM_001318374.2(PCDH9):​c.*10395_*10406dupATATATATATAT 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 0.022 (460 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 = 0.0223 (1982/89030) while in subpopulation NFE AF= 0.027 (1140/42238). AF 95% confidence interval is 0.0257. There are 460 homozygotes in gnomad4. There are 945 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1982 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH9	NM_203487.3	c.3036+10458_3036+10469dupATATATATATAT		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.*10395_*10406dupATATATATATAT		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000367092.3
PCDH9	ENST00000377865.7	c.3036+10458_3036+10469dupATATATATATAT		intron_variant	Intron 2 of 4	1	NM_203487.3	ENSP00000367096.2
PCDH9	ENST00000544246.5	c.3036+10458_3036+10469dupATATATATATAT		intron_variant	Intron 2 of 3	1		ENSP00000442186.2
PCDH9	ENST00000456367.5	c.3036+10458_3036+10469dupATATATATATAT		intron_variant	Intron 2 of 4	1		ENSP00000401699.2

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 1981 AN: 88986 Hom.: 460 Cov.: 0

Gnomad AFR AF: 0.0198

Gnomad AMI AF: 0.00288

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.0149

Gnomad SAS AF: 0.0165

Gnomad FIN AF: 0.00866

Gnomad MID AF: 0.0187

Gnomad NFE AF: 0.0270

Gnomad OTH AF: 0.0235

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0223 AC: 1982 AN: 89030 Hom.: 460 Cov.: 0 AF XY: 0.0221 AC XY: 945 AN XY: 42786

Gnomad4 AFR AF: 0.0198

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.00866

Gnomad4 NFE AF: 0.0270

Gnomad4 OTH AF: 0.0233

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;