Genetic Variant ATP8B4:n.*32G>T (chr15-50018938-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000558906.5(ATP8B4):n.*32G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 1,230,510 control chromosomes in the GnomAD database, including 158,779 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 0.58 ( 27071 hom., cov: 33)

Exomes 𝑓: 0.47 ( 131708 hom. )

Consequence

ATP8B4
ENST00000558906.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.266

Publications

4 publications found

Variant links:

Genes affected

ATP8B4 (HGNC:13536): (ATPase phospholipid transporting 8B4 (putative)) This gene encodes a member of the cation transport ATPase (P-type) family and type IV subfamily. The encoded protein is involved in phospholipid transport in the cell membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]

ATP8B4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4 link	c.363-8021G>T		intron_variant	Intron 6 of 27	ENST00000284509.11	NP_079113.2	Q8TF62Q6PG43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11 link	c.363-8021G>T		intron_variant	Intron 6 of 27	5	NM_024837.4	ENSP00000284509.6		Q8TF62

Frequencies

GnomAD3 genomes

AF:

0.578

AC:

87879

AN:

151948

Hom.:

27022

Cov.:

show subpopulations

Gnomad AFR

AF:

0.726

Gnomad AMI

AF:

0.512

Gnomad AMR

AF:

0.603

Gnomad ASJ

AF:

0.406

Gnomad EAS

AF:

0.993

Gnomad SAS

AF:

0.751

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.460

Gnomad OTH

AF:

0.543

GnomAD2 exomes

AF:

0.608

AC:

77813

AN:

127984

AF XY:

0.605

show subpopulations

Gnomad AFR exome

AF:

0.725

Gnomad AMR exome

AF:

0.705

Gnomad ASJ exome

AF:

0.400

Gnomad EAS exome

AF:

0.998

Gnomad FIN exome

AF:

0.496

Gnomad NFE exome

AF:

0.452

Gnomad OTH exome

AF:

0.513

GnomAD4 exome

AF:

0.475

AC:

511781

AN:

1078444

Hom.:

131708

Cov.:

AF XY:

0.483

AC XY:

256781

AN XY:

531492

show subpopulations

African (AFR)

AF:

0.731

AC:

16640

AN:

22770

American (AMR)

AF:

0.706

AC:

19871

AN:

28158

Ashkenazi Jewish (ASJ)

AF:

0.393

AC:

6142

AN:

15638

East Asian (EAS)

AF:

0.996

AC:

12366

AN:

12418

South Asian (SAS)

AF:

0.730

AC:

54423

AN:

74572

European-Finnish (FIN)

AF:

0.494

AC:

6232

AN:

12616

Middle Eastern (MID)

AF:

0.467

AC:

1996

AN:

4278

European-Non Finnish (NFE)

AF:

0.431

AC:

374153

AN:

868648

Other (OTH)

AF:

0.507

AC:

19958

AN:

39346

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.412

Heterozygous variant carriers

9652

19303

28955

38606

48258

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13092

26184

39276

52368

65460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.579

AC:

87992

AN:

152066

Hom.:

27071

Cov.:

AF XY:

0.586

AC XY:

43584

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.726

AC:

30149

AN:

41506

American (AMR)

AF:

0.604

AC:

9228

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.406

AC:

1409

AN:

3470

East Asian (EAS)

AF:

0.993

AC:

5145

AN:

5180

South Asian (SAS)

AF:

0.750

AC:

3618

AN:

4824

European-Finnish (FIN)

AF:

0.510

AC:

5364

AN:

10526

Middle Eastern (MID)

AF:

0.538

AC:

157

AN:

292

European-Non Finnish (NFE)

AF:

0.461

AC:

31300

AN:

67968

Other (OTH)

AF:

0.548

AC:

1155

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1791

3582

5372

7163

8954

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

738

1476

2214

2952

3690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.512

Hom.:

4710

Bravo

AF:

0.588

Asia WGS

AF:

0.870

AC:

3017

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.3

(source)

DANN

Benign

0.49

PhyloP100

-0.27

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over