rs9868128

Variant names:

• chr3-193581919-A-T
• rs9868128
• XM_047449063.1:c.-165-13T>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

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]

ENSG00000293063 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449483.1. 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
	ENSG00000293063	ENST00000449483.1	TSL:3	n.71-13T>A		intron	N/A
	ATP13A4	ENST00000489140.1	TSL:4	n.92-13T>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs9868128;

hg19: chr3-193299708;