Genetic Variant PCDH10-DT:n.306+53G>A (chr4-133145551-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000505289.6(PCDH10-DT):n.306+53G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.026 in 152,054 control chromosomes in the GnomAD database, including 92 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.026 ( 92 hom., cov: 31)

Failed GnomAD Quality Control

Consequence

PCDH10-DT
ENST00000505289.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.364

Publications

1 publications found

Variant links:

Genes affected

PCDH10-DT (HGNC:53036): (PCDH10 divergent transcript)

PCDH10-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH10-DT	NR_125885.1 link	n.308+53G>A		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PCDH10-DT	ENST00000505289.6 link	n.306+53G>A	intron_variant	Intron 3 of 7	1
PCDH10-DT	ENST00000509715.1 link	n.308+53G>A	intron_variant	Intron 3 of 4	4
PCDH10-DT	ENST00000656167.1 link	n.305+53G>A	intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes

AF:

0.0259

AC:

3942

AN:

151936

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0155

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0461

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.0731

Gnomad FIN

AF:

0.0428

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0150

Gnomad OTH

AF:

0.0230

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

GnomAD4 genome

AF:

0.0260

AC:

3959

AN:

152054

Hom.:

Cov.:

AF XY:

0.0292

AC XY:

2172

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.0157

AC:

651

AN:

41502

American (AMR)

AF:

0.0462

AC:

706

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

3468

East Asian (EAS)

AF:

0.127

AC:

655

AN:

5142

South Asian (SAS)

AF:

0.0733

AC:

352

AN:

4800

European-Finnish (FIN)

AF:

0.0428

AC:

453

AN:

10588

Middle Eastern (MID)

AF:

0.0137

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0150

AC:

1019

AN:

67978

Other (OTH)

AF:

0.0237

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

185

370

555

740

925

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<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:

0.0210

Hom.:

Bravo

AF:

0.0264

Asia WGS

AF:

0.101

AC:

351

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.0

(source)

DANN

Benign

0.50

PhyloP100

-0.36

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over