13-67214935-GATATATATATATATATATATATATATATAT-GATATATATATATATATATATATATATATATATATATATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_001318374.2(PCDH9):​c.*10397_*10406dupATATATATAT 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 0.026 ( 508 hom., cov: 0)

Consequence

PCDH9
NM_001318374.2 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.114
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0257 (2285/88998) while in subpopulation NFE AF= 0.0294 (1244/42254). AF 95% confidence interval is 0.0281. There are 508 homozygotes in gnomad4. There are 936 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2285 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PCDH9NM_203487.3 linkc.3036+10460_3036+10469dupATATATATAT intron_variant Intron 2 of 4 ENST00000377865.7 NP_982354.1 Q9HC56-1X5D7N0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCDH9ENST00000377861 linkc.*10397_*10406dupATATATATAT 3_prime_UTR_variant Exon 2 of 2 1 ENSP00000367092.3 Q5VT82
PCDH9ENST00000377865.7 linkc.3036+10460_3036+10469dupATATATATAT intron_variant Intron 2 of 4 1 NM_203487.3 ENSP00000367096.2 Q9HC56-1
PCDH9ENST00000544246.5 linkc.3036+10460_3036+10469dupATATATATAT intron_variant Intron 2 of 3 1 ENSP00000442186.2 Q9HC56-2
PCDH9ENST00000456367.5 linkc.3036+10460_3036+10469dupATATATATAT intron_variant Intron 2 of 4 1 ENSP00000401699.2 B7ZM79

Frequencies

GnomAD3 genomes
AF:
0.0257
AC:
2285
AN:
88956
Hom.:
507
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0287
Gnomad AMI
AF:
0.0375
Gnomad AMR
AF:
0.0188
Gnomad ASJ
AF:
0.0395
Gnomad EAS
AF:
0.00875
Gnomad SAS
AF:
0.0162
Gnomad FIN
AF:
0.00325
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0294
Gnomad OTH
AF:
0.0243
GnomAD4 exome
Cov.:
0
GnomAD4 genome
AF:
0.0257
AC:
2285
AN:
88998
Hom.:
508
Cov.:
0
AF XY:
0.0219
AC XY:
936
AN XY:
42734
show subpopulations
Gnomad4 AFR
AF:
0.0286
Gnomad4 AMR
AF:
0.0188
Gnomad4 ASJ
AF:
0.0395
Gnomad4 EAS
AF:
0.00877
Gnomad4 SAS
AF:
0.0158
Gnomad4 FIN
AF:
0.00325
Gnomad4 NFE
AF:
0.0294
Gnomad4 OTH
AF:
0.0259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs66460017; hg19: chr13-67789067; API