rs1960061

Variant names:

• chr13-26096236-C-T
• rs1960061
• ENST00000426792.2:n.1434-1410G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426792.2(ATP8A2P3):​n.1434-1410G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,966 control chromosomes in the GnomAD database, including 8,953 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 0.34 (8953 hom., cov: 32)
• Consequence: ATP8A2P3 ENST00000426792.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

ATP8A2P3 (HGNC:42641): (ATPase phospholipid transporting 8A2 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8A2P3	ENST00000426792.2	n.1434-1410G>A		intron_variant	Intron 16 of 16	6

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51706 AN: 151848 Hom.: 8949 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.340 AC: 51741 AN: 151966 Hom.: 8953 Cov.: 32 AF XY: 0.336 AC XY: 24938 AN XY: 74236

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.324

Alfa AF: 0.368 Hom.: 17460

Bravo AF: 0.337

Asia WGS AF: 0.315 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.061
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1960061; hg19: chr13-26670374;