rs5030981

Positions:

• chr16-67483851-G-A

Variant summary

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

The ENST00000602596.1(ATP6V0D1-DT):​n.137-259G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0812 in 152,966 control chromosomes in the GnomAD database, including 1,668 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 0.082 (1667 hom., cov: 32)
  • Exomes 𝑓: 0.016 (1 hom.)
• Consequence: ATP6V0D1-DT ENST00000602596.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460

Genes affected

ATP6V0D1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP6V0D1-DT	NR_184225.1	n.127-259G>A		intron_variant
ATP6V0D1-DT	NR_184226.1	n.127-259G>A		intron_variant
ATP6V0D1-DT	NR_184227.1	n.127-259G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP6V0D1-DT	ENST00000602596.1	n.137-259G>A		intron_variant		2
ATP6V0D1-DT	ENST00000635000.1	n.114-259G>A		intron_variant		5
ATP6V0D1-DT	ENST00000653151.2	n.152-259G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0815 AC: 12393 AN: 152054 Hom.: 1665 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00249

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00137

Gnomad OTH AF: 0.0522

GnomAD4 exome AF: 0.0164 AC: 13 AN: 794 Hom.: 1 Cov.: 0 AF XY: 0.0117 AC XY: 5 AN XY: 426

Gnomad4 AFR exome AF: 0.214

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0667

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0500

GnomAD4 genome AF: 0.0815 AC: 12408 AN: 152172 Hom.: 1667 Cov.: 32 AF XY: 0.0782 AC XY: 5819 AN XY: 74390

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.0308

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00137

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0707 Hom.: 141

Bravo AF: 0.0929

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5030981; hg19: chr16-67517754;