Variant rs7250872 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_138813.4(ATP8B3):c.133G>A(p.Gly45Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,611,692 control chromosomes in the GnomAD database, including 85,421 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.37 ( 10864 hom., cov: 33)

Exomes 𝑓: 0.31 ( 74557 hom. )

Consequence

ATP8B3
NM_138813.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Variant links:

Genes affected

ATP8B3 (HGNC:13535): (ATPase phospholipid transporting 8B3) 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 the other. This gene encodes member 3 of phospholipid-transporting ATPase 8B; other members of this protein family are located on chromosomes 1, 15 and 18. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ATP8B3 links:

ATP8B3 (HGNC:):

ATP8B3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=3.5777688E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATP8B3	NM_138813.4 linkuse as main transcript	c.133G>A	p.Gly45Arg	missense_variant	2/29	ENST00000310127.10	NP_620168.1	O60423-2
ATP8B3	NM_001178002.3 linkuse as main transcript	c.-27G>A		5_prime_UTR_variant	2/29		NP_001171473.1	O60423-3
ATP8B3	NR_047593.3 linkuse as main transcript	n.372G>A		non_coding_transcript_exon_variant	2/29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP8B3	ENST00000310127.10 linkuse as main transcript	c.133G>A	p.Gly45Arg	missense_variant	2/29	1	NM_138813.4	ENSP00000311336.6		O60423-2

Frequencies

GnomAD3 genomes

AF:

0.371

AC:

56402

AN:

151990

Hom.:

10855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.473

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.416

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.411

Gnomad SAS

AF:

0.324

Gnomad FIN

AF:

0.394

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.343

GnomAD3 exomes

AF:

0.347

AC:

85485

AN:

246628

Hom.:

15360

AF XY:

0.339

AC XY:

45554

AN XY:

134438

show subpopulations

Gnomad AFR exome

AF:

0.480

Gnomad AMR exome

AF:

0.423

Gnomad ASJ exome

AF:

0.288

Gnomad EAS exome

AF:

0.415

Gnomad SAS exome

AF:

0.318

Gnomad FIN exome

AF:

0.383

Gnomad NFE exome

AF:

0.301

Gnomad OTH exome

AF:

0.332

GnomAD4 exome

AF:

0.315

AC:

459207

AN:

1459584

Hom.:

74557

Cov.:

AF XY:

0.314

AC XY:

228144

AN XY:

726094

show subpopulations

Gnomad4 AFR exome

AF:

0.491

Gnomad4 AMR exome

AF:

0.421

Gnomad4 ASJ exome

AF:

0.286

Gnomad4 EAS exome

AF:

0.455

Gnomad4 SAS exome

AF:

0.320

Gnomad4 FIN exome

AF:

0.381

Gnomad4 NFE exome

AF:

0.297

Gnomad4 OTH exome

AF:

0.315

GnomAD4 genome

AF:

0.371

AC:

56445

AN:

152108

Hom.:

10864

Cov.:

AF XY:

0.374

AC XY:

27830

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.473

Gnomad4 AMR

AF:

0.416

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.412

Gnomad4 SAS

AF:

0.324

Gnomad4 FIN

AF:

0.394

Gnomad4 NFE

AF:

0.302

Gnomad4 OTH

AF:

0.344

Alfa

AF:

0.311

Hom.:

14813

Bravo

AF:

0.377

TwinsUK

AF:

0.290

AC:

1077

ALSPAC

AF:

0.297

AC:

1146

ESP6500AA

AF:

0.457

AC:

1898

ESP6500EA

AF:

0.298

AC:

2506

ExAC

AF:

0.344

AC:

41382

Asia WGS

AF:

0.352

AC:

1224

AN:

3478

EpiCase

AF:

0.290

EpiControl

AF:

0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.063

T;.

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0020

LIST_S2

Benign

0.38

T;T

MetaRNN

Benign

0.00036

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

1.4

L;.

PrimateAI

Benign

0.41

PROVEAN

Benign

-0.94

N;.

REVEL

Benign

0.12

Sift

Pathogenic

0.0

D;.

Sift4G

Uncertain

0.047

D;D

Polyphen

0.013

B;.

Vest4

0.033

MutPred

0.45

Gain of methylation at G45 (P = 0.0221);Gain of methylation at G45 (P = 0.0221);

MPC

0.092

ClinPred

0.011

GERP RS

1.4

Varity_R

0.10

gMVP

0.25

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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