chr15-49859332-G-A

Variant names:

• chr15-49859332-G-A
• rs1059850
• ENST00000558498.5:n.1713C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558498.5(ATP8B4):​n.1713C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,052 control chromosomes in the GnomAD database, including 6,845 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 0.29 (6845 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ATP8B4 ENST00000558498.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 4 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.*862C>T		3_prime_UTR_variant	Exon 28 of 28	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.*862C>T		3_prime_UTR_variant	Exon 28 of 28	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44308 AN: 151934 Hom.: 6833 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.286

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.292 AC: 44362 AN: 152052 Hom.: 6845 Cov.: 32 AF XY: 0.286 AC XY: 21291 AN XY: 74336

African (AFR) AF: 0.325 AC: 13459 AN: 41430

American (AMR) AF: 0.231 AC: 3532 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3464

East Asian (EAS) AF: 0.0316 AC: 164 AN: 5182

South Asian (SAS) AF: 0.267 AC: 1289 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2920 AN: 10570

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21074 AN: 67986

Other (OTH) AF: 0.284 AC: 599 AN: 2112

Alfa AF: 0.298 Hom.: 1140

Bravo AF: 0.286

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.19
DANN	Benign	0.71
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1059850; hg19: chr15-50151529;