3-194413986-C-A

Variant names:

• chr3-194413986-C-A
• rs10049106
• NM_001367549.1:c.3403-147G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001367549.1(ATP13A3):​c.3403-147G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATP13A3 NM_001367549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 2 publications found

Genes affected

ATP13A3 (HGNC:24113): (ATPase 13A3) ATP13A3 is a member of the P-type ATPase family of proteins that transport a variety of cations across membranes. Other P-type ATPases include ATP7B (MIM 606882) and ATP7A (MIM 300011).[supplied by OMIM, Aug 2008]

ATP13A3 Gene-Disease associations (from GenCC):

• pulmonary arterial hypertension

  Inheritance: SD Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367549.1. 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
	ATP13A3	NM_001367549.1	MANE Select	c.3403-147G>T		intron	N/A	NP_001354478.1	A0A2R8Y635
	ATP13A3	NM_001374836.1		c.3322-147G>T		intron	N/A	NP_001361765.1
	ATP13A3	NM_001437993.1		c.3403-147G>T		intron	N/A	NP_001424922.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP13A3	ENST00000645319.2	MANE Select	c.3403-147G>T		intron	N/A	ENSP00000494937.2	A0A2R8Y635
	ATP13A3	ENST00000429136.7	TSL:1	n.1249-147G>T		intron	N/A
	ATP13A3	ENST00000461660.2	TSL:1	n.507-147G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 516424 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 274142

African (AFR) AF: 0.00 AC: 0 AN: 14230

American (AMR) AF: 0.00 AC: 0 AN: 27994

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15582

East Asian (EAS) AF: 0.00 AC: 0 AN: 31882

South Asian (SAS) AF: 0.00 AC: 0 AN: 50404

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32406

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2760

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 312940

Other (OTH) AF: 0.00 AC: 0 AN: 28226

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.17
PhyloP100		-0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10049106; hg19: chr3-194134715;