rs11586379

Variant names:

• chr1-154335154-C-T
• rs11586379
• NM_001370597.1:c.837+563C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ATP8B2	NM_001370597.1	c.837+563C>T		intron_variant	Intron 11 of 27	ENST00000368489.6	NP_001357526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B2	ENST00000368489.6	c.837+563C>T		intron_variant	Intron 11 of 27	1	NM_001370597.1	ENSP00000357475.4

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

African (AFR) AF: 0.335 AC: 13882 AN: 41472

American (AMR) AF: 0.310 AC: 4736 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1296 AN: 5164

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4820

European-Finnish (FIN) AF: 0.236 AC: 2499 AN: 10590

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19454 AN: 67992

Other (OTH) AF: 0.295 AC: 621 AN: 2104

Alfa AF: 0.287 Hom.: 12769

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
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11586379; hg19: chr1-154307630;