13-67214935-G-GAT

Variant names:

• chr13-67214935-G-GAT
• rs66460017
• ENST00000377861:c.*10405_*10406dupAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001318374.2(PCDH9):​c.*10405_*10406dupAT 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 0.027 (316 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.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH9	NM_203487.3	c.3036+10468_3036+10469dupAT		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.*10405_*10406dupAT		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000367092.3
PCDH9	ENST00000377865.7	c.3036+10468_3036+10469dupAT		intron_variant	Intron 2 of 4	1	NM_203487.3	ENSP00000367096.2
PCDH9	ENST00000544246.5	c.3036+10468_3036+10469dupAT		intron_variant	Intron 2 of 3	1		ENSP00000442186.2
PCDH9	ENST00000456367.5	c.3036+10468_3036+10469dupAT		intron_variant	Intron 2 of 4	1		ENSP00000401699.2

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 2416 AN: 88920 Hom.: 316 Cov.: 0

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.0217

Gnomad AMR AF: 0.0138

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.00646

Gnomad FIN AF: 0.00907

Gnomad MID AF: 0.0123

Gnomad NFE AF: 0.0153

Gnomad OTH AF: 0.0217

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0272 AC: 2418 AN: 88962 Hom.: 316 Cov.: 0 AF XY: 0.0255 AC XY: 1090 AN XY: 42730

Gnomad4 AFR AF: 0.0643

Gnomad4 AMR AF: 0.0138

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.0160

Gnomad4 SAS AF: 0.00678

Gnomad4 FIN AF: 0.00907

Gnomad4 NFE AF: 0.0153

Gnomad4 OTH AF: 0.0216

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;