dbSNP rs4494482: ATP8B4:c.*225A>T (chr15-49859969-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_024837.4(ATP8B4):c.*225A>T variant causes a 3 prime UTR 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
NM_024837.4 3_prime_UTR

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024837.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ATP8B4	NM_024837.4	MANE Select	c.*225A>T	3_prime_UTR	Exon 28 of 28	NP_079113.2
ATP8B4	NR_073596.2		n.3856A>T	non_coding_transcript_exon	Exon 28 of 28
ATP8B4	NR_073597.2		n.3809A>T	non_coding_transcript_exon	Exon 27 of 27

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.*225A>T	3_prime_UTR	Exon 28 of 28	ENSP00000284509.6	Q8TF62
ATP8B4	ENST00000557955.5	TSL:1	n.*1502A>T	non_coding_transcript_exon	Exon 27 of 27	ENSP00000453690.1	H0YMP8
ATP8B4	ENST00000558498.5	TSL:1	n.1076A>T	non_coding_transcript_exon	Exon 5 of 5

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over