chr1-154346088-G-A

Position:

• chr1-154346088-G-A

Variant summary

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

The NM_001370597.1(ATP8B2):​c.2779-143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 1,252,374 control chromosomes in the GnomAD database, including 132,874 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 0.39 (13315 hom., cov: 31)
  • Exomes 𝑓: 0.46 (119559 hom.)
• Consequence: ATP8B2 NM_001370597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.923

Genes affected

ATP8B2 (HGNC:13534): (ATPase phospholipid transporting 8B2) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B2	NM_001370597.1	c.2779-143G>A		intron_variant		ENST00000368489.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B2	ENST00000368489.6	c.2779-143G>A		intron_variant		1	NM_001370597.1	P1
ATP8B2	ENST00000672630.1	c.2878-143G>A		intron_variant
ATP8B2	ENST00000696573.1	c.2836-143G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59657 AN: 151858 Hom.: 13316 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.447

GnomAD4 exome AF: 0.461 AC: 506830 AN: 1100398 Hom.: 119559 AF XY: 0.463 AC XY: 255724 AN XY: 552094

Gnomad4 AFR exome AF: 0.159

Gnomad4 AMR exome AF: 0.508

Gnomad4 ASJ exome AF: 0.582

Gnomad4 EAS exome AF: 0.602

Gnomad4 SAS exome AF: 0.492

Gnomad4 FIN exome AF: 0.429

Gnomad4 NFE exome AF: 0.458

Gnomad4 OTH exome AF: 0.460

GnomAD4 genome AF: 0.393 AC: 59676 AN: 151976 Hom.: 13315 Cov.: 31 AF XY: 0.395 AC XY: 29339 AN XY: 74286

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.441

Alfa AF: 0.435 Hom.: 8250

Bravo AF: 0.391

Asia WGS AF: 0.520 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.20

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: rs1194585; hg19: chr1-154318564; COSMIC: COSV59246352; COSMIC: COSV59246352;