rs10520028

Variant names:

• chr15-35811659-C-A
• rs10520028
• ENST00000501169.3:n.504-46328C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000501169.3(DPH6-DT):​n.504-46328C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00716 in 152,320 control chromosomes in the GnomAD database, including 12 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 0.0072 (12 hom., cov: 32)
• Consequence: DPH6-DT ENST00000501169.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 0 publications found

Genes affected

DPH6-DT (HGNC:44147): (DPH6 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00716 (1090/152320) while in subpopulation AMR AF = 0.0267 (409/15302). AF 95% confidence interval is 0.0246. There are 12 homozygotes in GnomAd4. There are 495 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPH6-DT	NR_038251.1	n.463-46328C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPH6-DT	ENST00000501169.3	n.504-46328C>A		intron_variant	Intron 2 of 2	1
DPH6-DT	ENST00000559210.1	n.177-46328C>A		intron_variant	Intron 2 of 2	3
DPH6-DT	ENST00000661846.2	n.402-45463C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.00714 AC: 1086 AN: 152202 Hom.: 11 Cov.: 32

Gnomad AFR AF: 0.00207

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.000942

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00763

Gnomad OTH AF: 0.00907

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

GnomAD4 genome AF: 0.00716 AC: 1090 AN: 152320 Hom.: 12 Cov.: 32 AF XY: 0.00665 AC XY: 495 AN XY: 74484

African (AFR) AF: 0.00207 AC: 86 AN: 41576

American (AMR) AF: 0.0267 AC: 409 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3472

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5176

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4824

European-Finnish (FIN) AF: 0.000942 AC: 10 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00763 AC: 519 AN: 68030

Other (OTH) AF: 0.00898 AC: 19 AN: 2116

Alfa AF: 0.00788 Hom.: 5

Bravo AF: 0.0101

Asia WGS AF: 0.00549 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.56
PhyloP100		-0.030
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10520028; hg19: chr15-36103860;