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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024837.4(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
NM_024837.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4 link	c.-79T>A		5_prime_UTR_variant	Exon 1 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.-79T>A		5_prime_UTR_variant	Exon 1 of 28	5	NM_024837.4	ENSP00000284509.6		Q8TF62

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

Gnomad4 AFR exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.269

AC:

40867

AN:

152034

Hom.:

6102

Cov.:

AF XY:

0.276

AC XY:

20527

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.330

Gnomad4 AMR

AF:

0.303

Gnomad4 ASJ

AF:

0.0879

Gnomad4 EAS

AF:

0.526

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.327

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.233

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.4

DANN

Benign

0.78

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over