dbSNP rs16963067: ATP8B4:c.2036-22A>G (chr15-49917061-T-C) – 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.2036-22A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,606,320 control chromosomes in the GnomAD database, including 26,435 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 0.23 ( 5881 hom., cov: 32)

Exomes 𝑓: 0.16 ( 20554 hom. )

Consequence

ATP8B4
NM_024837.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.869

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:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4 link	c.2036-22A>G		intron_variant	Intron 19 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.2036-22A>G		intron_variant	Intron 19 of 27	5	NM_024837.4	ENSP00000284509.6		Q8TF62

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35219

AN:

152024

Hom.:

5875

Cov.:

show subpopulations

Gnomad AFR

AF:

0.469

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.147

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.132

Gnomad FIN

AF:

0.0907

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.195

GnomAD2 exomes

AF:

0.149

AC:

37306

AN:

250682

AF XY:

0.146

show subpopulations

Gnomad AFR exome

AF:

0.478

Gnomad AMR exome

AF:

0.0950

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.00136

Gnomad FIN exome

AF:

0.0954

Gnomad NFE exome

AF:

0.154

Gnomad OTH exome

AF:

0.148

GnomAD4 exome

AF:

0.156

AC:

227573

AN:

1454178

Hom.:

20554

Cov.:

AF XY:

0.157

AC XY:

113410

AN XY:

723984

show subpopulations

African (AFR)

AF:

0.486

AC:

16188

AN:

33296

American (AMR)

AF:

0.102

AC:

4539

AN:

44672

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

3869

AN:

26092

East Asian (EAS)

AF:

0.00103

AC:

AN:

39654

South Asian (SAS)

AF:

0.143

AC:

12287

AN:

85976

European-Finnish (FIN)

AF:

0.0988

AC:

5256

AN:

53192

Middle Eastern (MID)

AF:

0.163

AC:

935

AN:

5748

European-Non Finnish (NFE)

AF:

0.158

AC:

174783

AN:

1105352

Other (OTH)

AF:

0.161

AC:

9675

AN:

60196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

9538

19075

28613

38150

47688

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6250

12500

18750

25000

31250

<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:

0.232

AC:

35264

AN:

152142

Hom.:

5881

Cov.:

AF XY:

0.224

AC XY:

16631

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.469

AC:

19449

AN:

41478

American (AMR)

AF:

0.147

AC:

2251

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.162

AC:

561

AN:

3466

East Asian (EAS)

AF:

0.00193

AC:

AN:

5186

South Asian (SAS)

AF:

0.132

AC:

637

AN:

4818

European-Finnish (FIN)

AF:

0.0907

AC:

963

AN:

10612

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10695

AN:

67986

Other (OTH)

AF:

0.192

AC:

403

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1251

2501

3752

5002

6253

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

346

692

1038

1384

1730

<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:

0.197

Hom.:

734

Bravo

AF:

0.246

Asia WGS

AF:

0.0790

AC:

275

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.24

(source)

DANN

Benign

0.46

PhyloP100

-0.87

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