rs10518629

Variant names:

• chr4-133142080-C-T
• rs10518629
• ENST00000505289.6:n.378+631G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PCDH10-DT	NR_125885.1	n.380+631G>A		intron_variant	Intron 4 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCDH10-DT	ENST00000505289.6	n.378+631G>A		intron_variant	Intron 4 of 7	1
PCDH10-DT	ENST00000509715.1	n.485+526G>A		intron_variant	Intron 4 of 4	4
PCDH10-DT	ENST00000656167.1	n.482+526G>A		intron_variant	Intron 4 of 8

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

African (AFR) AF: 0.175 AC: 7242 AN: 41388

American (AMR) AF: 0.369 AC: 5620 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1371 AN: 3460

East Asian (EAS) AF: 0.171 AC: 885 AN: 5164

South Asian (SAS) AF: 0.408 AC: 1967 AN: 4816

European-Finnish (FIN) AF: 0.402 AC: 4230 AN: 10526

Middle Eastern (MID) AF: 0.462 AC: 134 AN: 290

European-Non Finnish (NFE) AF: 0.445 AC: 30070 AN: 67534

Other (OTH) AF: 0.352 AC: 740 AN: 2102

Alfa AF: 0.411 Hom.: 7039

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
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs10518629; hg19: chr4-134063235;