rs10518629

Positions:

• chr4-133142080-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505289.6(PCDH10-DT):​n.378+631G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,418 control chromosomes in the GnomAD database, including 10,321 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 0.35 (10321 hom., cov: 32)
• Consequence: PCDH10-DT ENST00000505289.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845

Genes affected

PCDH10-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCDH10-DT	NR_125885.1	n.380+631G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCDH10-DT	ENST00000505289.6	n.378+631G>A		intron_variant		1
PCDH10-DT	ENST00000509715.1	n.485+526G>A		intron_variant		4
PCDH10-DT	ENST00000656167.1	n.482+526G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52810 AN: 151300 Hom.: 10323 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.458

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.349 AC: 52816 AN: 151418 Hom.: 10321 Cov.: 32 AF XY: 0.346 AC XY: 25596 AN XY: 74002

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.352

Alfa AF: 0.413 Hom.: 6127

Bravo AF: 0.337

Asia WGS AF: 0.270 AC: 937 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518629; hg19: chr4-134063235;