15-50018938-C-T

Variant names:

• chr15-50018938-C-T
• rs12591825
• NM_024837.4:c.363-8021G>A

Variant summary

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

The NM_024837.4(ATP8B4):​c.363-8021G>A variant causes a intron 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• 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: 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=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024837.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	NM_024837.4	MANE Select	c.363-8021G>A		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.554G>A		non_coding_transcript_exon	Exon 7 of 28
	ATP8B4	NR_073598.2		n.625G>A		non_coding_transcript_exon	Exon 7 of 29

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.363-8021G>A		intron	N/A	ENSP00000284509.6	Q8TF62
	ATP8B4	ENST00000558906.5	TSL:1	n.*32G>A		non_coding_transcript_exon	Exon 7 of 28	ENSP00000452956.1	H0YLJ1
	ATP8B4	ENST00000559726.5	TSL:1	n.*32G>A		non_coding_transcript_exon	Exon 7 of 29	ENSP00000453229.1	H0YLJ1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1099700 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 541346

African (AFR) AF: 0.00 AC: 0 AN: 22924

American (AMR) AF: 0.00 AC: 0 AN: 28192

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15800

East Asian (EAS) AF: 0.00 AC: 0 AN: 12422

South Asian (SAS) AF: 0.00 AC: 0 AN: 74870

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12628

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4324

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 888462

Other (OTH) AF: 0.00 AC: 0 AN: 40078

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.53
PhyloP100		-0.27

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: rs12591825; hg19: chr15-50311135;