3-193572723-A-T

Variant names:

• chr3-193572723-A-T
• rs11922359
• XM_047449063.1:c.35+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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000489140.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP13A4	ENST00000489140.1	TSL:4	n.291+8984T>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11922359;

hg19: chr3-193290512;