rs5030981

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_184227.1(ATP6V0D1-DT):​n.127-259G>A 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 0.0812 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
NR_184227.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.460
Variant links:
Genes affected
ATP6V0D1-DT (HGNC:55268): (ATP6V0D1 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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-DTNR_184227.1 linkuse as main transcriptn.127-259G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATP6V0D1-DTENST00000656196.1 linkuse as main transcriptn.207-259G>A intron_variant, non_coding_transcript_variant

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs5030981; hg19: chr16-67517754; API