Genetic Variant PCDH9:c.*10385_*10406delATATATATATATATATATATAT (chr13-67214935-GATATATATATATATATATATAT-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001318374.2(PCDH9):c.*10385_*10406delATATATATATATATATATATAT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.011 ( 121 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

PCDH9
NM_001318374.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.719

Publications

0 publications found

Variant links:

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]

PCDH9 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High AC in GnomAd4 at 952 AD gene.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PCDH9	NM_203487.3	MANE Select	c.3036+10448_3036+10469delATATATATATATATATATATAT	intron	N/A	NP_982354.1	X5D7N0
PCDH9	NM_001318374.2		c.10385_10406delATATATATATATATATATATAT	3_prime_UTR	Exon 2 of 2	NP_001305303.1	Q5VT82
PCDH9	NM_020403.5		c.3036+10448_3036+10469delATATATATATATATATATATAT	intron	N/A	NP_065136.1	Q9HC56-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PCDH9	ENST00000377861.4	TSL:1	c.10385_10406delATATATATATATATATATATAT	3_prime_UTR	Exon 2 of 2	ENSP00000367092.3	Q5VT82
PCDH9	ENST00000377865.7	TSL:1 MANE Select	c.3036+10448_3036+10469delATATATATATATATATATATAT	intron	N/A	ENSP00000367096.2	Q9HC56-1
PCDH9	ENST00000544246.5	TSL:1	c.3036+10448_3036+10469delATATATATATATATATATATAT	intron	N/A	ENSP00000442186.2	Q9HC56-2

Frequencies

GnomAD3 genomes

AF:

0.0107

AC:

953

AN:

89252

Hom.:

121

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00872

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00903

Gnomad ASJ

AF:

0.00604

Gnomad EAS

AF:

0.000324

Gnomad SAS

AF:

0.00161

Gnomad FIN

AF:

0.0171

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0133

Gnomad OTH

AF:

0.00520

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0107

AC:

952

AN:

89294

Hom.:

121

Cov.:

AF XY:

0.0101

AC XY:

432

AN XY:

42910

show subpopulations

African (AFR)

AF:

0.00866

AC:

195

AN:

22508

American (AMR)

AF:

0.00902

AC:

AN:

8208

Ashkenazi Jewish (ASJ)

AF:

0.00604

AC:

AN:

2484

East Asian (EAS)

AF:

0.000325

AC:

AN:

3080

South Asian (SAS)

AF:

0.00161

AC:

AN:

3104

European-Finnish (FIN)

AF:

0.0171

AC:

AN:

5562

Middle Eastern (MID)

AF:

0.00

AC:

AN:

154

European-Non Finnish (NFE)

AF:

0.0133

AC:

561

AN:

42336

Other (OTH)

AF:

0.00515

AC:

AN:

1164

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.650

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.72

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over