rs10520028

chr15-35811659-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_038251.1(DPH6-DT):n.463-46328C>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 0.00716 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 NR_038251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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=-0.82).
• 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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPH6-DT	NR_038251.1	n.463-46328C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPH6-DT	ENST00000501169.3	n.504-46328C>A		intron_variant, non_coding_transcript_variant		1
DPH6-DT	ENST00000559210.1	n.177-46328C>A		intron_variant, non_coding_transcript_variant		3
DPH6-DT	ENST00000661846.1	n.100-45463C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00207

Gnomad4 AMR AF: 0.0267

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.00348

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.000942

Gnomad4 NFE AF: 0.00763

Gnomad4 OTH AF: 0.00898

Alfa AF: 0.00771 Hom.: 2

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520028; hg19: chr15-36103860;