rs7694118

Variant names:

• chr4-133147480-G-A
• rs7694118
• ENST00000505289.6:n.87-204C>T

Variant summary

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

The ENST00000670166.1(PCDH10-DT):​n.201C>T variant causes a non coding transcript exon 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 ENST00000670166.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.56
• Publications: 8 publications found

Genes affected

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670166.1. 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
	PCDH10-DT	NR_125885.1		n.89-204C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDH10-DT	ENST00000505289.6	TSL:1	n.87-204C>T		intron	N/A
	PCDH10-DT	ENST00000670166.1		n.201C>T		non_coding_transcript_exon	Exon 1 of 8
	PCDH10-DT	ENST00000732795.1		n.666C>T		non_coding_transcript_exon	Exon 1 of 8

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29635 AN: 152090 Hom.: 6416 Cov.: 33

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.: 33 AF XY: 0.195 AC XY: 14542 AN XY: 74402

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: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0290 AC: 1975 AN: 68022

Other (OTH) AF: 0.157 AC: 333 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Uncertain	-0.070
CADD	Benign	19
DANN	Benign	0.86
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs7694118; hg19: chr4-134068635;