rs5030981

Variant names:

• chr16-67483851-G-A
• rs5030981
• ENST00000602596.1:n.137-259G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ATP6V0D1-DT (HGNC:55268): (ATP6V0D1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATP6V0D1-DT	NR_184225.1	n.127-259G>A		intron_variant	Intron 1 of 3
ATP6V0D1-DT	NR_184226.1	n.127-259G>A		intron_variant	Intron 1 of 3
ATP6V0D1-DT	NR_184227.1	n.127-259G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP6V0D1-DT	ENST00000602596.1	n.137-259G>A		intron_variant	Intron 1 of 1	2
ATP6V0D1-DT	ENST00000635000.1	n.114-259G>A		intron_variant	Intron 1 of 3	5
ATP6V0D1-DT	ENST00000653151.3	n.190-259G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.214 AC: 9 AN: 42

American (AMR) AF: 0.00 AC: 0 AN: 20

Ashkenazi Jewish (ASJ) AF: 0.0667 AC: 2 AN: 30

East Asian (EAS) AF: 0.00 AC: 0 AN: 26

South Asian (SAS) AF: 0.00 AC: 0 AN: 14

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 576

Other (OTH) AF: 0.0500 AC: 2 AN: 40

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

African (AFR) AF: 0.282 AC: 11709 AN: 41468

American (AMR) AF: 0.0308 AC: 470 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00374 AC: 13 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00207 AC: 10 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10604

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00137 AC: 93 AN: 68020

Other (OTH) AF: 0.0512 AC: 108 AN: 2110

Alfa AF: 0.166 Hom.: 658

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
PhyloP100		-0.46
PromoterAI		0.022	Neutral

Splicing

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

Other links and lift over

dbSNP: rs5030981; hg19: chr16-67517754;