Genetic Variant ATP8B4:c.*201G>A (chr15-49859993-C-T) – 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.*201G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 557,848 control chromosomes in the GnomAD database, including 19,059 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 0.25 ( 5114 hom., cov: 32)

Exomes 𝑓: 0.25 ( 13945 hom. )

Consequence

ATP8B4
NM_024837.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00800

Publications

6 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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.*201G>A	3_prime_UTR	Exon 28 of 28	NP_079113.2
ATP8B4	NR_073596.2		n.3832G>A	non_coding_transcript_exon	Exon 28 of 28
ATP8B4	NR_073597.2		n.3785G>A	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.*201G>A	3_prime_UTR	Exon 28 of 28	ENSP00000284509.6	Q8TF62
ATP8B4	ENST00000557955.5	TSL:1	n.*1478G>A	non_coding_transcript_exon	Exon 27 of 27	ENSP00000453690.1	H0YMP8
ATP8B4	ENST00000558498.5	TSL:1	n.1052G>A	non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38593

AN:

151584

Hom.:

5105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.0415

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.260

GnomAD4 exome

AF:

0.248

AC:

100772

AN:

406154

Hom.:

13945

Cov.:

AF XY:

0.248

AC XY:

51587

AN XY:

208036

show subpopulations

African (AFR)

AF:

0.255

AC:

2723

AN:

10680

American (AMR)

AF:

0.178

AC:

2081

AN:

11688

Ashkenazi Jewish (ASJ)

AF:

0.243

AC:

2866

AN:

11792

East Asian (EAS)

AF:

0.0165

AC:

445

AN:

27028

South Asian (SAS)

AF:

0.226

AC:

5146

AN:

22744

European-Finnish (FIN)

AF:

0.267

AC:

6961

AN:

26116

Middle Eastern (MID)

AF:

0.306

AC:

587

AN:

1920

European-Non Finnish (NFE)

AF:

0.273

AC:

74090

AN:

270960

Other (OTH)

AF:

0.253

AC:

5873

AN:

23226

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

3541

7081

10622

14162

17703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

928

1856

2784

3712

4640

<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:

0.255

AC:

38628

AN:

151694

Hom.:

5114

Cov.:

AF XY:

0.250

AC XY:

18502

AN XY:

74070

show subpopulations

African (AFR)

AF:

0.262

AC:

10819

AN:

41344

American (AMR)

AF:

0.213

AC:

3247

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

820

AN:

3468

East Asian (EAS)

AF:

0.0412

AC:

212

AN:

5150

South Asian (SAS)

AF:

0.221

AC:

1061

AN:

4800

European-Finnish (FIN)

AF:

0.254

AC:

2657

AN:

10448

Middle Eastern (MID)

AF:

0.253

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.278

AC:

18856

AN:

67944

Other (OTH)

AF:

0.256

AC:

540

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1478

2956

4434

5912

7390

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<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:

0.261

Hom.:

14512

Bravo

AF:

0.249

Asia WGS

AF:

0.121

AC:

423

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.3

(source)

DANN

Benign

0.69

PhyloP100

-0.0080

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