rs10090327

Variant names:

• chr8-86033676-A-C
• rs10090327
• ENST00000521564.1:c.-262-32712A>C

Variant summary

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

The ENST00000521564.1(ATP6V0D2):​c.-262-32712A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,186 control chromosomes in the GnomAD database, including 4,733 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 0.24 (4733 hom., cov: 32)
• Consequence: ATP6V0D2 ENST00000521564.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

Genes affected

ATP6V0D2 (HGNC:18266): (ATPase H+ transporting V0 subunit d2) Predicted to enable proton transmembrane transporter activity. Predicted to be involved in vacuolar acidification and vacuolar transport. Located in apical plasma membrane. Part of vacuolar proton-transporting V-type ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP6V0D2	ENST00000521564.1	c.-262-32712A>C		intron_variant	Intron 1 of 3	3		ENSP00000429731.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35774 AN: 152068 Hom.: 4736 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.235 AC: 35774 AN: 152186 Hom.: 4733 Cov.: 32 AF XY: 0.234 AC XY: 17439 AN XY: 74396

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.258

Alfa AF: 0.266 Hom.: 4875

Bravo AF: 0.231

Asia WGS AF: 0.329 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10090327; hg19: chr8-87045905;