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GeneBe

19-1783078-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_138813.4(ATP8B3):c.3853C>T(p.Leu1285=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00466 in 1,613,014 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 5 hom., cov: 31)
Exomes 𝑓: 0.0048 ( 41 hom. )

Consequence

ATP8B3
NM_138813.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.515
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 19-1783078-G-A is Benign according to our data. Variant chr19-1783078-G-A is described in ClinVar as [Benign]. Clinvar id is 783072.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.515 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ATP8B3NM_138813.4 linkuse as main transcriptc.3853C>T p.Leu1285= synonymous_variant 29/29 ENST00000310127.10
ATP8B3NM_001178002.3 linkuse as main transcriptc.3742C>T p.Leu1248= synonymous_variant 29/29
ATP8B3NR_047593.3 linkuse as main transcriptn.4236C>T non_coding_transcript_exon_variant 29/29

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ATP8B3ENST00000310127.10 linkuse as main transcriptc.3853C>T p.Leu1285= synonymous_variant 29/291 NM_138813.4 A2O60423-2
ATP8B3ENST00000525591.5 linkuse as main transcriptc.3742C>T p.Leu1248= synonymous_variant 29/291 P2O60423-3
ATP8B3ENST00000531925.5 linkuse as main transcriptc.*3736C>T 3_prime_UTR_variant, NMD_transcript_variant 29/292

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00371
AC:
563
AN:
151912
Hom.:
5
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000677
Gnomad AMI
AF:
0.0340
Gnomad AMR
AF:
0.000394
Gnomad ASJ
AF:
0.00231
Gnomad EAS
AF:
0.000194
Gnomad SAS
AF:
0.00229
Gnomad FIN
AF:
0.0127
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00502
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.00347
AC:
859
AN:
247428
Hom.:
2
AF XY:
0.00355
AC XY:
477
AN XY:
134492
show subpopulations
Gnomad AFR exome
AF:
0.000984
Gnomad AMR exome
AF:
0.000466
Gnomad ASJ exome
AF:
0.00110
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00171
Gnomad FIN exome
AF:
0.0121
Gnomad NFE exome
AF:
0.00434
Gnomad OTH exome
AF:
0.00316
GnomAD4 exome
AF:
0.00476
AC:
6951
AN:
1460984
Hom.:
41
Cov.:
31
AF XY:
0.00468
AC XY:
3403
AN XY:
726736
show subpopulations
Gnomad4 AFR exome
AF:
0.000568
Gnomad4 AMR exome
AF:
0.000426
Gnomad4 ASJ exome
AF:
0.00195
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00181
Gnomad4 FIN exome
AF:
0.0126
Gnomad4 NFE exome
AF:
0.00522
Gnomad4 OTH exome
AF:
0.00386
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00370
AC:
563
AN:
152030
Hom.:
5
Cov.:
31
AF XY:
0.00394
AC XY:
293
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.000675
Gnomad4 AMR
AF:
0.000393
Gnomad4 ASJ
AF:
0.00231
Gnomad4 EAS
AF:
0.000194
Gnomad4 SAS
AF:
0.00229
Gnomad4 FIN
AF:
0.0127
Gnomad4 NFE
AF:
0.00502
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00359
Hom.:
0
Bravo
AF:
0.00284
EpiCase
AF:
0.00398
EpiControl
AF:
0.00440

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
0.088
Dann
Benign
0.46

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.

Other links and lift over

dbSNP: rs141089151; hg19: chr19-1783077; API