7-138798082-G-A

Variant names:

• chr7-138798082-G-A
• rs199654929
• NM_020632.3:c.-169C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_020632.3(ATP6V0A4):​c.-169C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,584,796 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0023 (2 hom., cov: 30)
  • Exomes 𝑓: 0.00093 (20 hom.)
• Consequence: ATP6V0A4 NM_020632.3 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.62

Genes affected

ATP6V0A4 (HGNC:866): (ATPase H+ transporting V0 subunit a4) This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular compartments of eukaryotic cells. V-ATPase dependent acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c'', and d. This gene is one of four genes in man and mouse that encode different isoforms of the a subunit. Alternatively spliced transcript variants encoding the same protein have been described. Mutations in this gene are associated with renal tubular acidosis associated with preserved hearing. [provided by RefSeq, Jul 2008]

TMEM213 (HGNC:27220): (transmembrane protein 213) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 7-138798082-G-A is Benign according to our data. Variant chr7-138798082-G-A is described in ClinVar as [Benign]. Clinvar id is 359037.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00226 (344/152238) while in subpopulation AMR AF= 0.0195 (298/15290). AF 95% confidence interval is 0.0177. There are 2 homozygotes in gnomad4. There are 186 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP6V0A4	NM_020632.3	c.-169C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 22	ENST00000310018.7	NP_065683.2
ATP6V0A4	NM_020632.3	c.-169C>T		5_prime_UTR_variant	Exon 1 of 22	ENST00000310018.7	NP_065683.2
TMEM213	NM_001085429.2	c.-23G>A		5_prime_UTR_variant	Exon 1 of 3	ENST00000442682.7	NP_001078898.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP6V0A4	ENST00000310018.7	c.-169C>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 22	1	NM_020632.3	ENSP00000308122.2
ATP6V0A4	ENST00000310018.7	c.-169C>T		5_prime_UTR_variant	Exon 1 of 22	1	NM_020632.3	ENSP00000308122.2
TMEM213	ENST00000442682.7	c.-23G>A		5_prime_UTR_variant	Exon 1 of 3	1	NM_001085429.2	ENSP00000390407.2

Frequencies

GnomAD3 genomes AF: 0.00225 AC: 343 AN: 152120 Hom.: 3 Cov.: 30

Gnomad AFR AF: 0.000749

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.00287

GnomAD3 exomes AF: 0.00531 AC: 1073 AN: 202038 Hom.: 18 AF XY: 0.00390 AC XY: 426 AN XY: 109130

Gnomad AFR exome AF: 0.000620

Gnomad AMR exome AF: 0.0357

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000112

Gnomad NFE exome AF: 0.000112

Gnomad OTH exome AF: 0.00346

GnomAD4 exome AF: 0.000933 AC: 1337 AN: 1432558 Hom.: 20 Cov.: 31 AF XY: 0.000769 AC XY: 546 AN XY: 709888

Gnomad4 AFR exome AF: 0.000335

Gnomad4 AMR exome AF: 0.0310

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000156

Gnomad4 NFE exome AF: 0.0000382

Gnomad4 OTH exome AF: 0.000741

GnomAD4 genome AF: 0.00226 AC: 344 AN: 152238 Hom.: 2 Cov.: 30 AF XY: 0.00250 AC XY: 186 AN XY: 74428

Gnomad4 AFR AF: 0.000746

Gnomad4 AMR AF: 0.0195

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.000103

Gnomad4 OTH AF: 0.00284

Alfa AF: 0.00105 Hom.: 0

Bravo AF: 0.00364

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Autosomal recessive distal renal tubular acidosis Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.044
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs199654929; hg19: chr7-138482827;