rs1960061

Positions:

• chr13-26096236-C-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8A2P3	ENST00000426792.2	n.1434-1410G>A		intron_variant, non_coding_transcript_variant

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;