rs13139219

Variant names:

• chr4-42451286-A-C
• rs13139219
• NM_006095.2:c.2896+695T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-42451286-A-C
• chr4-42451286-A-G

Variant summary

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

The NM_006095.2(ATP8A1):​c.2896+695T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,946 control chromosomes in the GnomAD database, including 31,862 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 0.63 (31862 hom., cov: 30)
• Consequence: ATP8A1 NM_006095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 5 publications found

Genes affected

ATP8A1 (HGNC:13531): (ATPase phospholipid transporting 8A1) The P-type adenosinetriphosphatases (P-type ATPases) are a family of proteins which use the free energy of ATP hydrolysis to drive uphill transport of ions across membranes. Several subfamilies of P-type ATPases have been identified. One subfamily catalyzes transport of heavy metal ions. Another subfamily transports non-heavy metal ions (NMHI). The protein encoded by this gene is a member of the third subfamily of P-type ATPases and acts to transport amphipaths, such as phosphatidylserine. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006095.2. 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
	ATP8A1	NM_006095.2	MANE Select	c.2896+695T>G		intron	N/A	NP_006086.1	Q9Y2Q0-1
	ATP8A1	NM_001400024.1		c.2896+695T>G		intron	N/A	NP_001386953.1
	ATP8A1	NM_001400025.1		c.2872+695T>G		intron	N/A	NP_001386954.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8A1	ENST00000381668.9	TSL:1 MANE Select	c.2896+695T>G		intron	N/A	ENSP00000371084.5	Q9Y2Q0-1
	ATP8A1	ENST00000264449.14	TSL:1	c.2851+695T>G		intron	N/A	ENSP00000264449.10	Q9Y2Q0-3
	ATP8A1	ENST00000514372.5	TSL:1	n.*548+695T>G		intron	N/A	ENSP00000426495.1	H0YAA1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95358 AN: 151828 Hom.: 31865 Cov.: 30

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.628 AC: 95377 AN: 151946 Hom.: 31862 Cov.: 30 AF XY: 0.632 AC XY: 46979 AN XY: 74276

African (AFR) AF: 0.375 AC: 15525 AN: 41408

American (AMR) AF: 0.666 AC: 10161 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2541 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3845 AN: 5160

South Asian (SAS) AF: 0.600 AC: 2893 AN: 4820

European-Finnish (FIN) AF: 0.810 AC: 8554 AN: 10554

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49803 AN: 67964

Other (OTH) AF: 0.668 AC: 1409 AN: 2108

Alfa AF: 0.695 Hom.: 117477

Bravo AF: 0.612

Asia WGS AF: 0.617 AC: 2145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.013
DANN	Benign	0.26
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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: rs13139219; hg19: chr4-42453303;