chr13-67214935-G-GAT

Variant names:

• chr13-67214935-G-GAT
• rs66460017
• ENST00000377861.4:c.*10405_*10406dupAT

Variant summary

Our verdict is Benign. The variant received -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
• 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: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318374.2. 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+10468_3036+10469dupAT		intron	N/A	NP_982354.1	X5D7N0
	PCDH9	NM_001318374.2		c.*10405_*10406dupAT		3_prime_UTR	Exon 2 of 2	NP_001305303.1	Q5VT82
	PCDH9	NM_020403.5		c.3036+10468_3036+10469dupAT		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.*10405_*10406dupAT		3_prime_UTR	Exon 2 of 2	ENSP00000367092.3	Q5VT82
	PCDH9	ENST00000377865.7	TSL:1 MANE Select	c.3036+10468_3036+10469dupAT		intron	N/A	ENSP00000367096.2	Q9HC56-1
	PCDH9	ENST00000544246.5	TSL:1	c.3036+10468_3036+10469dupAT		intron	N/A	ENSP00000442186.2	Q9HC56-2

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

African (AFR) AF: 0.0643 AC: 1437 AN: 22348

American (AMR) AF: 0.0138 AC: 113 AN: 8178

Ashkenazi Jewish (ASJ) AF: 0.0234 AC: 58 AN: 2482

East Asian (EAS) AF: 0.0160 AC: 49 AN: 3062

South Asian (SAS) AF: 0.00678 AC: 21 AN: 3096

European-Finnish (FIN) AF: 0.00907 AC: 50 AN: 5512

Middle Eastern (MID) AF: 0.0132 AC: 2 AN: 152

European-Non Finnish (NFE) AF: 0.0153 AC: 648 AN: 42280

Other (OTH) AF: 0.0216 AC: 25 AN: 1160

Alfa AF: 0.00 Hom.: 0

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; COSMIC: COSV60602251;