Variant 1-154344677-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001370597.1(ATP8B2):c.2178C>T(p.Ser726Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 1,610,510 control chromosomes in the GnomAD database, including 171,551 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 ( 13308 hom., cov: 31)

Exomes 𝑓: 0.46 ( 158243 hom. )

Consequence

ATP8B2
NM_001370597.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.68

Variant links:

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]

ATP8B2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP7

Synonymous conserved (PhyloP=-3.68 with no splicing effect.

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	Protein	UniProt
ATP8B2	NM_001370597.1 link	c.2178C>T	p.Ser726Ser	synonymous_variant	21/28	ENST00000368489.6	NP_001357526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ATP8B2	ENST00000368489.6 link	c.2178C>T	p.Ser726Ser	synonymous_variant	21/28	1	NM_001370597.1	ENSP00000357475.4	A0A5K1VW70
ATP8B2	ENST00000672630.1 link	c.2277C>T	p.Ser759Ser	synonymous_variant	21/28			ENSP00000500034.1	P98198-3
ATP8B2	ENST00000696573.1 link	c.2235C>T	p.Ser745Ser	synonymous_variant	20/27			ENSP00000512728.1	P98198-1

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59648

AN:

151878

Hom.:

13309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.488

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.601

Gnomad EAS

AF:

0.607

Gnomad SAS

AF:

0.518

Gnomad FIN

AF:

0.419

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.463

Gnomad OTH

AF:

0.447

GnomAD3 exomes

AF:

0.470

AC:

118017

AN:

251300

Hom.:

28903

AF XY:

0.475

AC XY:

64529

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.156

Gnomad AMR exome

AF:

0.506

Gnomad ASJ exome

AF:

0.583

Gnomad EAS exome

AF:

0.607

Gnomad SAS exome

AF:

0.495

Gnomad FIN exome

AF:

0.422

Gnomad NFE exome

AF:

0.473

Gnomad OTH exome

AF:

0.479

GnomAD4 exome

AF:

0.462

AC:

673183

AN:

1458514

Hom.:

158243

Cov.:

AF XY:

0.464

AC XY:

336278

AN XY:

724806

show subpopulations

Gnomad4 AFR exome

AF:

0.157

Gnomad4 AMR exome

AF:

0.507

Gnomad4 ASJ exome

AF:

0.582

Gnomad4 EAS exome

AF:

0.601

Gnomad4 SAS exome

AF:

0.493

Gnomad4 FIN exome

AF:

0.428

Gnomad4 NFE exome

AF:

0.460

Gnomad4 OTH exome

AF:

0.460

GnomAD4 genome

AF:

0.393

AC:

59665

AN:

151996

Hom.:

13308

Cov.:

AF XY:

0.395

AC XY:

29323

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.490

Gnomad4 ASJ

AF:

0.601

Gnomad4 EAS

AF:

0.608

Gnomad4 SAS

AF:

0.518

Gnomad4 FIN

AF:

0.419

Gnomad4 NFE

AF:

0.463

Gnomad4 OTH

AF:

0.441

Alfa

AF:

0.451

Hom.:

22922

Bravo

AF:

0.391

Asia WGS

AF:

0.520

AC:

1808

AN:

3478

EpiCase

AF:

0.474

EpiControl

AF:

0.482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.16

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over