rs13338499

Positions:

• chr16-67486220-A-G
• chr16-67486220-A-T

Variant summary

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

The NR_184227.1(ATP6V0D1-DT):​n.345+1892A>G 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 0.266 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 NR_184227.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP6V0D1-DT	NR_184227.1	n.345+1892A>G		intron_variant, non_coding_transcript_variant
ATP6V0D1-DT	NR_184225.1	n.345+1892A>G		intron_variant, non_coding_transcript_variant
ATP6V0D1-DT	NR_184226.1	n.345+1892A>G		intron_variant, non_coding_transcript_variant
ATP6V0D1-DT	NR_184228.1	n.549+1688A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP6V0D1-DT	ENST00000656196.1	n.425+1892A>G		intron_variant, non_coding_transcript_variant
ATP6V0D1-DT	ENST00000602476.1	n.88-594A>G		intron_variant, non_coding_transcript_variant		3
ATP6V0D1-DT	ENST00000635000.1	n.332+1892A>G		intron_variant, non_coding_transcript_variant		5
ATP6V0D1-DT	ENST00000659360.1	n.366+1892A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0864

Gnomad4 EAS AF: 0.0163

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.223

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13338499; hg19: chr16-67520123;