15-49859993-C-T

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00800
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]

Genome browser will be placed here

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 (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ATP8B4NM_024837.4 linkc.*201G>A 3_prime_UTR_variant Exon 28 of 28 ENST00000284509.11 NP_079113.2 Q8TF62Q6PG43

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ATP8B4ENST00000284509 linkc.*201G>A 3_prime_UTR_variant Exon 28 of 28 5 NM_024837.4 ENSP00000284509.6 Q8TF62

Frequencies

GnomAD3 genomes
AF:
0.255
AC:
38593
AN:
151584
Hom.:
5105
Cov.:
32
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.:
6
AF XY:
0.248
AC XY:
51587
AN XY:
208036
show subpopulations
Gnomad4 AFR exome
AF:
0.255
Gnomad4 AMR exome
AF:
0.178
Gnomad4 ASJ exome
AF:
0.243
Gnomad4 EAS exome
AF:
0.0165
Gnomad4 SAS exome
AF:
0.226
Gnomad4 FIN exome
AF:
0.267
Gnomad4 NFE exome
AF:
0.273
Gnomad4 OTH exome
AF:
0.253
GnomAD4 genome
AF:
0.255
AC:
38628
AN:
151694
Hom.:
5114
Cov.:
32
AF XY:
0.250
AC XY:
18502
AN XY:
74070
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.213
Gnomad4 ASJ
AF:
0.236
Gnomad4 EAS
AF:
0.0412
Gnomad4 SAS
AF:
0.221
Gnomad4 FIN
AF:
0.254
Gnomad4 NFE
AF:
0.278
Gnomad4 OTH
AF:
0.256
Alfa
AF:
0.260
Hom.:
8827
Bravo
AF:
0.249
Asia WGS
AF:
0.121
AC:
423
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.3
DANN
Benign
0.69

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.

Other links and lift over

dbSNP: rs4544192; hg19: chr15-50152190; API