3-193581919-A-T

Variant names:

• chr3-193581919-A-T
• rs9868128
• ENST00000449483.1:n.71-13T>A

Variant summary

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

The ENST00000449483.1(ENSG00000293063):​n.71-13T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,728 control chromosomes in the GnomAD database, including 21,481 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 0.52 (21478 hom., cov: 29)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: ENSG00000293063 ENST00000449483.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 6 publications found

Genes affected

ENSG00000293063 (HGNC:):

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP13A4	XM_047449063.1	c.-165-13T>A		intron_variant	Intron 1 of 31		XP_047305019.1
ATP13A4	XM_017007319.2	c.-165-13T>A		intron_variant	Intron 1 of 26		XP_016862808.2
ATP13A4	XR_007095757.1	n.100-13T>A		intron_variant	Intron 1 of 25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293063	ENST00000449483.1	n.71-13T>A		intron_variant	Intron 1 of 2	3
ATP13A4	ENST00000489140.1	n.92-13T>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79264 AN: 151604 Hom.: 21445 Cov.: 29

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.492

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 6 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.523 AC: 79349 AN: 151722 Hom.: 21478 Cov.: 29 AF XY: 0.523 AC XY: 38757 AN XY: 74132

African (AFR) AF: 0.655 AC: 27097 AN: 41370

American (AMR) AF: 0.453 AC: 6899 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3468

East Asian (EAS) AF: 0.398 AC: 2052 AN: 5160

South Asian (SAS) AF: 0.434 AC: 2080 AN: 4798

European-Finnish (FIN) AF: 0.573 AC: 6009 AN: 10488

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31844 AN: 67898

Other (OTH) AF: 0.493 AC: 1038 AN: 2104

Alfa AF: 0.511 Hom.: 2510

Bravo AF: 0.522

Asia WGS AF: 0.430 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.4
DANN	Benign	0.83
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs9868128; hg19: chr3-193299708;