15-35566382-A-G

Position:

• chr15-35566382-A-G

Variant summary

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

The NR_038251.1(DPH6-DT):​n.279+19909A>G 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 0.733 in 152,122 control chromosomes in the GnomAD database, including 41,267 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 0.73 (41267 hom., cov: 33)
• Consequence: DPH6-DT NR_038251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPH6-DT	NR_038251.1	n.279+19909A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPH6-DT	ENST00000501169.3	n.320+19909A>G		intron_variant, non_coding_transcript_variant		1
DPH6-DT	ENST00000559210.1	n.91+19909A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111461 AN: 152004 Hom.: 41237 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.733 AC: 111540 AN: 152122 Hom.: 41267 Cov.: 33 AF XY: 0.740 AC XY: 55057 AN XY: 74360

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.740

Alfa AF: 0.756 Hom.: 86670

Bravo AF: 0.725

Asia WGS AF: 0.790 AC: 2745 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6495785; hg19: chr15-35858583;