3-193572723-A-T

Variant names:

• chr3-193572723-A-T
• rs11922359
• ENST00000489140.1:n.291+8984T>A

Variant summary

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

The ENST00000489140.1(ATP13A4):​n.291+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 ENST00000489140.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATP13A4	XM_047449063.1	c.35+8984T>A		intron_variant	Intron 2 of 31		XP_047305019.1
ATP13A4	XM_017007319.2	c.35+8984T>A		intron_variant	Intron 2 of 26		XP_016862808.2
ATP13A4	XR_007095757.1	n.299+8984T>A		intron_variant	Intron 2 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP13A4	ENST00000489140.1	n.291+8984T>A		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.620 AC: 25655 AN: 41386

American (AMR) AF: 0.352 AC: 5373 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1160 AN: 3468

East Asian (EAS) AF: 0.293 AC: 1514 AN: 5166

South Asian (SAS) AF: 0.400 AC: 1925 AN: 4808

European-Finnish (FIN) AF: 0.414 AC: 4359 AN: 10536

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20589 AN: 67934

Other (OTH) AF: 0.358 AC: 755 AN: 2106

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
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs11922359; hg19: chr3-193290512;