rs2947253

chr15-35757291-G-A

Variant summary

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

The NR_038251.1(DPH6-DT):n.462+45402G>A 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 0.895 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 NR_038251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DPH6-DT	NR_038251.1	n.462+45402G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPH6-DT	ENST00000501169.3	n.503+45402G>A		intron_variant, non_coding_transcript_variant		1
DPH6-DT	ENST00000559210.1	n.176+45500G>A		intron_variant, non_coding_transcript_variant		3
DPH6-DT	ENST00000661846.1	n.99+45402G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.808

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.884

Alfa AF: 0.888 Hom.: 27321

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2947253; hg19: chr15-36049492;