Genetic Variant ATP8B4:n.-79T>A (chr15-50119159-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000284509.11(ATP8B4):c.-79T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,100 control chromosomes in the GnomAD database, including 6,104 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 0.27 ( 6102 hom., cov: 32)

Exomes 𝑓: 0.21 ( 2 hom. )

Consequence

ATP8B4
ENST00000284509.11 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

3 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 (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000284509.11. 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.-79T>A	5_prime_UTR	Exon 1 of 28	NP_079113.2
ATP8B4	NR_073596.2		n.75T>A	non_coding_transcript_exon	Exon 1 of 28
ATP8B4	NR_073597.2		n.75T>A	non_coding_transcript_exon	Exon 1 of 27

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ATP8B4	ENST00000557955.5	TSL:1	n.-79T>A	non_coding_transcript_exon	Exon 1 of 27	ENSP00000453690.1
ATP8B4	ENST00000558906.5	TSL:1	n.-79T>A	non_coding_transcript_exon	Exon 1 of 28	ENSP00000452956.1
ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.-79T>A	5_prime_UTR	Exon 1 of 28	ENSP00000284509.6

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40828

AN:

151914

Hom.:

6093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.0879

Gnomad EAS

AF:

0.526

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.327

Gnomad MID

AF:

0.115

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.231

GnomAD4 exome

AF:

0.212

AC:

AN:

Hom.:

Cov.:

AF XY:

0.159

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.180

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.269

AC:

40867

AN:

152034

Hom.:

6102

Cov.:

AF XY:

0.276

AC XY:

20527

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.330

AC:

13676

AN:

41446

American (AMR)

AF:

0.303

AC:

4633

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0879

AC:

305

AN:

3470

East Asian (EAS)

AF:

0.526

AC:

2698

AN:

5128

South Asian (SAS)

AF:

0.267

AC:

1289

AN:

4820

European-Finnish (FIN)

AF:

0.327

AC:

3457

AN:

10578

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

14029

AN:

67986

Other (OTH)

AF:

0.233

AC:

492

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1471

2942

4413

5884

7355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

424

848

1272

1696

2120

<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:

0.239

Hom.:

640

Bravo

AF:

0.275

Asia WGS

AF:

0.384

AC:

1333

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.4

(source)

DANN

Benign

0.78

PhyloP100

-1.2

PromoterAI

-0.021

Neutral

(source)

Mutation Taster

=300/0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over