rs9868128

Positions:

• chr3-193581919-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.-165-13T>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: ATP13A4 XM_047449063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

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]

EEF1A1P23 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ATP13A4	XM_047449063.1	c.-165-13T>A		intron_variant			XP_047305019.1
ATP13A4	XM_017007319.2	c.-165-13T>A		intron_variant			XP_016862808.2
ATP13A4	XR_007095757.1	n.100-13T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EEF1A1P23	ENST00000449483.1	n.71-13T>A		intron_variant		3
ATP13A4	ENST00000489140.1	n.92-13T>A		intron_variant		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

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 1.00

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

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.493

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9868128; hg19: chr3-193299708;