Variant 19-1784891-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_138813.4(ATP8B3):c.3588T>C(p.Ser1196Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,612,062 control chromosomes in the GnomAD database, including 179,781 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 0.47 ( 16906 hom., cov: 33)

Exomes 𝑓: 0.47 ( 162875 hom. )

Consequence

ATP8B3
NM_138813.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP7

Synonymous conserved (PhyloP=-0.412 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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.3588T>C	p.Ser1196Ser	synonymous_variant	28/29	ENST00000310127.10	NP_620168.1	O60423-2
ATP8B3	NM_001178002.3 linkuse as main transcript	c.3477T>C	p.Ser1159Ser	synonymous_variant	28/29		NP_001171473.1	O60423-3
ATP8B3	NR_047593.3 linkuse as main transcript	n.3971T>C		non_coding_transcript_exon_variant	28/29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ATP8B3	ENST00000310127.10 linkuse as main transcript	c.3588T>C	p.Ser1196Ser	synonymous_variant	28/29	1	NM_138813.4	ENSP00000311336.6	O60423-2
ATP8B3	ENST00000525591.5 linkuse as main transcript	c.3477T>C	p.Ser1159Ser	synonymous_variant	28/29	1		ENSP00000437115.1	O60423-3
ATP8B3	ENST00000531925.5 linkuse as main transcript	n.*3471T>C		non_coding_transcript_exon_variant	28/29	2		ENSP00000444334.1	F5GZM8
ATP8B3	ENST00000531925.5 linkuse as main transcript	n.*3471T>C		3_prime_UTR_variant	28/29	2		ENSP00000444334.1	F5GZM8

Frequencies

GnomAD3 genomes

AF:

0.467

AC:

71002

AN:

151930

Hom.:

16890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.497

Gnomad AMI

AF:

0.501

Gnomad AMR

AF:

0.423

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.290

Gnomad SAS

AF:

0.462

Gnomad FIN

AF:

0.397

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.514

GnomAD3 exomes

AF:

0.447

AC:

109827

AN:

245792

Hom.:

25071

AF XY:

0.451

AC XY:

60338

AN XY:

133718

show subpopulations

Gnomad AFR exome

AF:

0.495

Gnomad AMR exome

AF:

0.394

Gnomad ASJ exome

AF:

0.503

Gnomad EAS exome

AF:

0.282

Gnomad SAS exome

AF:

0.468

Gnomad FIN exome

AF:

0.404

Gnomad NFE exome

AF:

0.479

Gnomad OTH exome

AF:

0.474

GnomAD4 exome

AF:

0.469

AC:

684840

AN:

1460014

Hom.:

162875

Cov.:

AF XY:

0.469

AC XY:

340836

AN XY:

726196

show subpopulations

Gnomad4 AFR exome

AF:

0.488

Gnomad4 AMR exome

AF:

0.398

Gnomad4 ASJ exome

AF:

0.508

Gnomad4 EAS exome

AF:

0.266

Gnomad4 SAS exome

AF:

0.470

Gnomad4 FIN exome

AF:

0.410

Gnomad4 NFE exome

AF:

0.480

Gnomad4 OTH exome

AF:

0.478

GnomAD4 genome

AF:

0.467

AC:

71061

AN:

152048

Hom.:

16906

Cov.:

AF XY:

0.459

AC XY:

34149

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.423

Gnomad4 ASJ

AF:

0.510

Gnomad4 EAS

AF:

0.290

Gnomad4 SAS

AF:

0.463

Gnomad4 FIN

AF:

0.397

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.509

Alfa

AF:

0.483

Hom.:

21229

Bravo

AF:

0.469

Asia WGS

AF:

0.391

AC:

1363

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.072

DANN

Benign

0.45

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

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