chr15-49859066-G-A

Variant names:

• chr15-49859066-G-A
• rs1059852
• ENST00000558498.5:n.1979C>T

Variant summary

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

The ENST00000558498.5(ATP8B4):​n.1979C>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 0.209 in 151,912 control chromosomes in the GnomAD database, including 3,649 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 0.21 (3649 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ATP8B4 ENST00000558498.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558498.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	NM_024837.4	MANE Select	c.*1128C>T		3_prime_UTR	Exon 28 of 28	NP_079113.2
	ATP8B4	NR_073596.2		n.4759C>T		non_coding_transcript_exon	Exon 28 of 28
	ATP8B4	NR_073597.2		n.4712C>T		non_coding_transcript_exon	Exon 27 of 27

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000558498.5	TSL:1	n.1979C>T		non_coding_transcript_exon	Exon 5 of 5
	ATP8B4	ENST00000559726.5	TSL:1	n.*4426C>T		non_coding_transcript_exon	Exon 29 of 29	ENSP00000453229.1
	ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.*1128C>T		3_prime_UTR	Exon 28 of 28	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31707 AN: 151794 Hom.: 3642 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.229

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: 0.209 AC: 31737 AN: 151912 Hom.: 3649 Cov.: 32 AF XY: 0.205 AC XY: 15252 AN XY: 74238

African (AFR) AF: 0.131 AC: 5451 AN: 41468

American (AMR) AF: 0.192 AC: 2932 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3470

East Asian (EAS) AF: 0.0217 AC: 112 AN: 5168

South Asian (SAS) AF: 0.176 AC: 848 AN: 4810

European-Finnish (FIN) AF: 0.235 AC: 2476 AN: 10524

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18241 AN: 67896

Other (OTH) AF: 0.226 AC: 478 AN: 2114

Alfa AF: 0.244 Hom.: 6340

Bravo AF: 0.200

Asia WGS AF: 0.0870 AC: 305 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.23
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: rs1059852; hg19: chr15-50151263;