ENST00000557955.5:n.*1502A>T – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000557955.5(ATP8B4):n.*1502A>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 0.247 in 478,878 control chromosomes in the GnomAD database, including 16,169 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 0.26 ( 5127 hom., cov: 32)

Exomes 𝑓: 0.24 ( 11042 hom. )

Consequence

ATP8B4
ENST00000557955.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.489

Publications

7 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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4 link	c.*225A>T		3_prime_UTR_variant	Exon 28 of 28	ENST00000284509.11	NP_079113.2	Q8TF62Q6PG43

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11 link	c.*225A>T		3_prime_UTR_variant	Exon 28 of 28	5	NM_024837.4	ENSP00000284509.6		Q8TF62

Frequencies

GnomAD3 genomes

AF:

0.256

AC:

38618

AN:

151030

Hom.:

5118

Cov.:

show subpopulations

Gnomad AFR

AF:

0.262

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.0417

Gnomad SAS

AF:

0.221

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.279

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.260

GnomAD4 exome

AF:

0.243

AC:

79668

AN:

327752

Hom.:

11042

Cov.:

AF XY:

0.244

AC XY:

40921

AN XY:

167876

show subpopulations

African (AFR)

AF:

0.254

AC:

2264

AN:

8922

American (AMR)

AF:

0.179

AC:

1937

AN:

10808

Ashkenazi Jewish (ASJ)

AF:

0.242

AC:

2587

AN:

10698

East Asian (EAS)

AF:

0.0149

AC:

379

AN:

25490

South Asian (SAS)

AF:

0.228

AC:

3505

AN:

15398

European-Finnish (FIN)

AF:

0.266

AC:

6282

AN:

23618

Middle Eastern (MID)

AF:

0.305

AC:

489

AN:

1604

European-Non Finnish (NFE)

AF:

0.271

AC:

57145

AN:

211134

Other (OTH)

AF:

0.253

AC:

5080

AN:

20080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2724

5448

8171

10895

13619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.256

AC:

38653

AN:

151126

Hom.:

5127

Cov.:

AF XY:

0.251

AC XY:

18520

AN XY:

73760

show subpopulations

African (AFR)

AF:

0.263

AC:

10823

AN:

41168

American (AMR)

AF:

0.214

AC:

3250

AN:

15174

Ashkenazi Jewish (ASJ)

AF:

0.237

AC:

822

AN:

3468

East Asian (EAS)

AF:

0.0414

AC:

212

AN:

5126

South Asian (SAS)

AF:

0.222

AC:

1064

AN:

4786

European-Finnish (FIN)

AF:

0.260

AC:

2665

AN:

10258

Middle Eastern (MID)

AF:

0.261

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.278

AC:

18860

AN:

67850

Other (OTH)

AF:

0.257

AC:

541

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1469

2937

4406

5874

7343

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.254

Hom.:

646

Bravo

AF:

0.249

Asia WGS

AF:

0.121

AC:

424

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.4

(source)

DANN

Benign

0.68

PhyloP100

-0.49

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