rs7694118

Positions:

• chr4-133147480-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_125885.1(PCDH10-DT):​n.89-204C>T variant causes a intron, non coding transcript 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 NR_125885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.56

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PCDH10-DT	NR_125885.1	n.89-204C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCDH10-DT	ENST00000667505.1	n.120-204C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.0746

Gnomad4 FIN AF: 0.0631

Gnomad4 NFE AF: 0.0290

Gnomad4 OTH AF: 0.157

Alfa AF: 0.172 Hom.: 1152

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	19
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7694118; hg19: chr4-134068635;