chr16-67486220-A-G

Variant names:

• chr16-67486220-A-G
• rs13338499
• ENST00000602476.1:n.88-594A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000602476.1(ATP6V0D1-DT):​n.88-594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 140,432 control chromosomes in the GnomAD database, including 8,619 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 0.27 (8619 hom., cov: 27)
• Consequence: ATP6V0D1-DT ENST00000602476.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 14 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000602476.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP6V0D1-DT	NR_184225.1		n.345+1892A>G		intron	N/A
	ATP6V0D1-DT	NR_184226.1		n.345+1892A>G		intron	N/A
	ATP6V0D1-DT	NR_184227.1		n.345+1892A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP6V0D1-DT	ENST00000602476.1	TSL:3	n.88-594A>G		intron	N/A
	ATP6V0D1-DT	ENST00000635000.1	TSL:5	n.332+1892A>G		intron	N/A
	ATP6V0D1-DT	ENST00000656196.1		n.425+1892A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 37250 AN: 140344 Hom.: 8586 Cov.: 27

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.0160

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.266 AC: 37327 AN: 140432 Hom.: 8619 Cov.: 27 AF XY: 0.264 AC XY: 18045 AN XY: 68454

African (AFR) AF: 0.633 AC: 24933 AN: 39416

American (AMR) AF: 0.140 AC: 1922 AN: 13692

Ashkenazi Jewish (ASJ) AF: 0.0864 AC: 283 AN: 3276

East Asian (EAS) AF: 0.0163 AC: 72 AN: 4430

South Asian (SAS) AF: 0.184 AC: 800 AN: 4348

European-Finnish (FIN) AF: 0.171 AC: 1559 AN: 9140

Middle Eastern (MID) AF: 0.305 AC: 67 AN: 220

European-Non Finnish (NFE) AF: 0.113 AC: 7155 AN: 63158

Other (OTH) AF: 0.223 AC: 429 AN: 1926

Alfa AF: 0.0867 Hom.: 240

Bravo AF: 0.263

Asia WGS AF: 0.141 AC: 487 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.14
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs13338499; hg19: chr16-67520123;