Variant 19-1783237-TCTC-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PM4_SupportingBP6_ModerateBS2

The NM_138813.4(ATP8B3):c.3691_3693del(p.Glu1231del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00355 in 1,610,048 control chromosomes in the GnomAD database, including 21 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0036 ( 20 hom. )

Consequence

ATP8B3
NM_138813.4 inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0900

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_138813.4. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 19-1783237-TCTC-T is Benign according to our data. Variant chr19-1783237-TCTC-T is described in ClinVar as [Likely_benign]. Clinvar id is 716789.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ATP8B3	NM_138813.4 linkuse as main transcript	c.3691_3693del	p.Glu1231del	inframe_deletion	29/29	ENST00000310127.10	NP_620168.1
ATP8B3	NM_001178002.3 linkuse as main transcript	c.3580_3582del	p.Glu1194del	inframe_deletion	29/29		NP_001171473.1
ATP8B3	NR_047593.3 linkuse as main transcript	n.4074_4076del		non_coding_transcript_exon_variant	29/29

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATP8B3	ENST00000310127.10 linkuse as main transcript	c.3691_3693del	p.Glu1231del	inframe_deletion	29/29	1	NM_138813.4	ENSP00000311336	A2	O60423-2
ATP8B3	ENST00000525591.5 linkuse as main transcript	c.3580_3582del	p.Glu1194del	inframe_deletion	29/29	1		ENSP00000437115	P2	O60423-3
ATP8B3	ENST00000531925.5 linkuse as main transcript	c.3574_3576del		3_prime_UTR_variant, NMD_transcript_variant	29/29	2		ENSP00000444334

Frequencies

GnomAD3 genomes

AF:

0.00308

AC:

465

AN:

151092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000925

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.000725

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00316

Gnomad FIN

AF:

0.00134

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00543

Gnomad OTH

AF:

0.00194

GnomAD3 exomes

AF:

0.00286

AC:

695

AN:

243066

Hom.:

AF XY:

0.00307

AC XY:

406

AN XY:

132262

show subpopulations

Gnomad AFR exome

AF:

0.000670

Gnomad AMR exome

AF:

0.000945

Gnomad ASJ exome

AF:

0.00142

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00258

Gnomad FIN exome

AF:

0.00198

Gnomad NFE exome

AF:

0.00459

Gnomad OTH exome

AF:

0.00286

GnomAD4 exome

AF:

0.00360

AC:

5247

AN:

1458838

Hom.:

AF XY:

0.00344

AC XY:

2496

AN XY:

725480

show subpopulations

Gnomad4 AFR exome

AF:

0.000508

Gnomad4 AMR exome

AF:

0.000836

Gnomad4 ASJ exome

AF:

0.00177

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00266

Gnomad4 FIN exome

AF:

0.00242

Gnomad4 NFE exome

AF:

0.00416

Gnomad4 OTH exome

AF:

0.00279

GnomAD4 genome

AF:

0.00308

AC:

466

AN:

151210

Hom.:

Cov.:

AF XY:

0.00267

AC XY:

197

AN XY:

73838

show subpopulations

Gnomad4 AFR

AF:

0.000923

Gnomad4 AMR

AF:

0.000724

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.000196

Gnomad4 SAS

AF:

0.00337

Gnomad4 FIN

AF:

0.00134

Gnomad4 NFE

AF:

0.00543

Gnomad4 OTH

AF:

0.00192

Alfa

AF:

0.00330

Hom.:

Bravo

AF:

0.00274

Asia WGS

AF:

0.00260

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over