ENST00000558906.5:n.*19T>A

Variant names:

• chr15-50018951-A-T
• rs11070741
• ENST00000558906.5:n.*19T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000558906.5(ATP8B4):​n.*19T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATP8B4 ENST00000558906.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 3 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558906.5. 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.363-8034T>A		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.541T>A		non_coding_transcript_exon	Exon 7 of 28
	ATP8B4	NR_073598.2		n.612T>A		non_coding_transcript_exon	Exon 7 of 29

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000558906.5	TSL:1	n.*19T>A		non_coding_transcript_exon	Exon 7 of 28	ENSP00000452956.1
	ATP8B4	ENST00000559726.5	TSL:1	n.*19T>A		non_coding_transcript_exon	Exon 7 of 29	ENSP00000453229.1
	ATP8B4	ENST00000558906.5	TSL:1	n.*19T>A		3_prime_UTR	Exon 7 of 28	ENSP00000452956.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1095866 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 539770

African (AFR) AF: 0.00 AC: 0 AN: 22780

American (AMR) AF: 0.00 AC: 0 AN: 28178

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15764

East Asian (EAS) AF: 0.00 AC: 0 AN: 12382

South Asian (SAS) AF: 0.00 AC: 0 AN: 74782

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4310

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 885138

Other (OTH) AF: 0.00 AC: 0 AN: 39914

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 5219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.60
PhyloP100		0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs11070741; hg19: chr15-50311148;