ENST00000501169.3:n.321-45082C>T

Variant names:

• chr15-35666625-C-T
• rs949867
• ENST00000501169.3:n.321-45082C>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000501169.3(DPH6-DT):​n.321-45082C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0191 in 152,236 control chromosomes in the GnomAD database, including 47 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 0.019 (47 hom., cov: 33)
• Consequence: DPH6-DT ENST00000501169.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0191 (2911/152236) while in subpopulation AFR AF= 0.0413 (1714/41540). AF 95% confidence interval is 0.0396. There are 47 homozygotes in gnomad4. There are 1420 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPH6-DT	NR_038251.1	n.280-45082C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPH6-DT	ENST00000501169.3	n.321-45082C>T		intron_variant	Intron 1 of 2	1
DPH6-DT	ENST00000559210.1	n.92-45082C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0191 AC: 2903 AN: 152118 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00825

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.00669

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00975

Gnomad OTH AF: 0.0186

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

GnomAD4 genome AF: 0.0191 AC: 2911 AN: 152236 Hom.: 47 Cov.: 33 AF XY: 0.0191 AC XY: 1420 AN XY: 74426

Gnomad4 AFR AF: 0.0413

Gnomad4 AMR AF: 0.00824

Gnomad4 ASJ AF: 0.0276

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.00669

Gnomad4 NFE AF: 0.00975

Gnomad4 OTH AF: 0.0184

Alfa AF: 0.00774 Hom.: 0

Bravo AF: 0.0186

Asia WGS AF: 0.0180 AC: 62 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	15
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs949867; hg19: chr15-35958826;