3-193572723-A-T

Position:

• chr3-193572723-A-T

Variant summary

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

The XM_047449063.1(ATP13A4):​c.35+8984T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,886 control chromosomes in the GnomAD database, including 13,978 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 0.41 (13978 hom., cov: 30)
• Consequence: ATP13A4 XM_047449063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

Genes affected

ATP13A4 (HGNC:25422): (ATPase 13A4) Predicted to enable ATPase-coupled cation transmembrane transporter activity. Predicted to be involved in cellular calcium ion homeostasis. Predicted to be located in endoplasmic reticulum membrane and endosome membrane. [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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP13A4	XM_017007319.2	c.35+8984T>A		intron_variant
ATP13A4	XM_047449063.1	c.35+8984T>A		intron_variant
ATP13A4	XR_007095757.1	n.299+8984T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP13A4	ENST00000489140.1	n.291+8984T>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61552 AN: 151768 Hom.: 13948 Cov.: 30

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.406 AC: 61642 AN: 151886 Hom.: 13978 Cov.: 30 AF XY: 0.409 AC XY: 30344 AN XY: 74208

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.358

Alfa AF: 0.371 Hom.: 1415

Bravo AF: 0.409

Asia WGS AF: 0.369 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11922359; hg19: chr3-193290512;