rs2947253

Variant names:

• chr15-35757291-G-A
• rs2947253
• ENST00000501169.3:n.503+45402G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000501169.3(DPH6-DT):​n.503+45402G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,166 control chromosomes in the GnomAD database, including 61,136 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 0.89 (61136 hom., cov: 32)
• Consequence: DPH6-DT ENST00000501169.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 4 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=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPH6-DT	NR_038251.1	n.462+45402G>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.503+45402G>A		intron_variant	Intron 2 of 2	1
DPH6-DT	ENST00000559210.1	n.176+45500G>A		intron_variant	Intron 2 of 2	3
DPH6-DT	ENST00000661846.2	n.401+45402G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136011 AN: 152048 Hom.: 61086 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.937

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.895 AC: 136114 AN: 152166 Hom.: 61136 Cov.: 32 AF XY: 0.890 AC XY: 66218 AN XY: 74388

African (AFR) AF: 0.961 AC: 39941 AN: 41550

American (AMR) AF: 0.808 AC: 12334 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2853 AN: 3472

East Asian (EAS) AF: 0.802 AC: 4136 AN: 5160

South Asian (SAS) AF: 0.889 AC: 4288 AN: 4824

European-Finnish (FIN) AF: 0.873 AC: 9262 AN: 10606

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60330 AN: 67966

Other (OTH) AF: 0.884 AC: 1865 AN: 2110

Alfa AF: 0.886 Hom.: 40162

Bravo AF: 0.893

Asia WGS AF: 0.850 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	14
DANN	Benign	0.63
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2947253; hg19: chr15-36049492;