dbSNP rs7694118: PCDH10-DT:n.87-204C>T (chr4-133147480-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000505289.6(PCDH10-DT):n.87-204C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,208 control chromosomes in the GnomAD database, including 6,448 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 6448 hom., cov: 33)

Consequence

PCDH10-DT
ENST00000505289.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.56

Publications

8 publications found

Variant links:

Genes affected

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

PCDH10-DT links:

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ACMG classification

Classification was made for transcript

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

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH10-DT	NR_125885.1 link	n.89-204C>T		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PCDH10-DT	ENST00000505289.6 link	n.87-204C>T	intron_variant	Intron 1 of 7	1
PCDH10-DT	ENST00000670166.1 link	n.201C>T	non_coding_transcript_exon_variant	Exon 1 of 8
PCDH10-DT	ENST00000732795.1 link	n.666C>T	non_coding_transcript_exon_variant	Exon 1 of 8

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29635

AN:

152090

Hom.:

6416

Cov.:

show subpopulations

Gnomad AFR

AF:

0.527

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.0403

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.0756

Gnomad FIN

AF:

0.0631

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.0290

Gnomad OTH

AF:

0.159

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

GnomAD4 genome

AF:

0.195

AC:

29707

AN:

152208

Hom.:

6448

Cov.:

AF XY:

0.195

AC XY:

14542

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.528

AC:

21906

AN:

41512

American (AMR)

AF:

0.178

AC:

2719

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0403

AC:

140

AN:

3472

East Asian (EAS)

AF:

0.307

AC:

1580

AN:

5150

South Asian (SAS)

AF:

0.0746

AC:

360

AN:

4826

European-Finnish (FIN)

AF:

0.0631

AC:

670

AN:

10614

Middle Eastern (MID)

AF:

0.0822

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0290

AC:

1975

AN:

68022

Other (OTH)

AF:

0.157

AC:

333

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

867

1734

2600

3467

4334

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.193

Hom.:

2276

Bravo

AF:

0.225

Asia WGS

AF:

0.227

AC:

787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

-0.070

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

3.6

Splicing

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

Publications

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rs7694118

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