rs11586379

chr1-154335154-C-T

Variant summary

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

The NM_001370597.1(ATP8B2):c.837+563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,094 control chromosomes in the GnomAD database, including 6,787 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 0.30 (6787 hom., cov: 32)
• Consequence: ATP8B2 NM_001370597.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B2	NM_001370597.1	c.837+563C>T		intron_variant		ENST00000368489.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B2	ENST00000368489.6	c.837+563C>T		intron_variant		1	NM_001370597.1	P1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44969 AN: 151976 Hom.: 6783 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.296 AC: 44996 AN: 152094 Hom.: 6787 Cov.: 32 AF XY: 0.296 AC XY: 21981 AN XY: 74358

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.295

Alfa AF: 0.287 Hom.: 8299

Bravo AF: 0.302

Asia WGS AF: 0.300 AC: 1042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	7.8
Dann	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs11586379; hg19: chr1-154307630;