3-194406320-C-T

Variant names:

• chr3-194406320-C-T
• rs13324377
• NM_001367549.1:c.3574-204G>A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001367549.1(ATP13A3):​c.3574-204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,956 control chromosomes in the GnomAD database, including 14,484 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.37 (14484 hom., cov: 32)
• Consequence: ATP13A3 NM_001367549.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.03

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BP6: Variant 3-194406320-C-T is Benign according to our data. Variant chr3-194406320-C-T is described in ClinVar as [Benign]. Clinvar id is 1252466.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP13A3	NM_001367549.1	c.3574-204G>A		intron_variant	Intron 33 of 33	ENST00000645319.2	NP_001354478.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP13A3	ENST00000645319.2	c.3574-204G>A		intron_variant	Intron 33 of 33		NM_001367549.1	ENSP00000494937.2

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55967 AN: 151838 Hom.: 14438 Cov.: 32

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.367

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.369 AC: 56066 AN: 151956 Hom.: 14484 Cov.: 32 AF XY: 0.367 AC XY: 27276 AN XY: 74276

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.366

Alfa AF: 0.282 Hom.: 1084

Bravo AF: 0.390

Asia WGS AF: 0.370 AC: 1288 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 10, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.47

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

Publications

LitVar

Other links and lift over

dbSNP: rs13324377; hg19: chr3-194127049;