chr15-50105307-C-T

Variant names:

• chr15-50105307-C-T
• rs6493402
• NM_024837.4:c.28+1632G>A

Variant summary

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

The NM_024837.4(ATP8B4):​c.28+1632G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 149,110 control chromosomes in the GnomAD database, including 39,301 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 0.72 (39301 hom., cov: 25)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

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.28+1632G>A		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.181+1632G>A		intron	N/A
	ATP8B4	NR_073597.2		n.181+1632G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.28+1632G>A		intron	N/A	ENSP00000284509.6	Q8TF62
	ATP8B4	ENST00000557955.5	TSL:1	n.28+1632G>A		intron	N/A	ENSP00000453690.1	H0YMP8
	ATP8B4	ENST00000558906.5	TSL:1	n.28+1632G>A		intron	N/A	ENSP00000452956.1	H0YLJ1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 107480 AN: 149018 Hom.: 39254 Cov.: 25

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.556

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.702

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.721 AC: 107574 AN: 149110 Hom.: 39301 Cov.: 25 AF XY: 0.720 AC XY: 52189 AN XY: 72464

African (AFR) AF: 0.861 AC: 34862 AN: 40472

American (AMR) AF: 0.728 AC: 10882 AN: 14942

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2074 AN: 3456

East Asian (EAS) AF: 0.699 AC: 3549 AN: 5076

South Asian (SAS) AF: 0.685 AC: 3242 AN: 4730

European-Finnish (FIN) AF: 0.639 AC: 6107 AN: 9564

Middle Eastern (MID) AF: 0.542 AC: 154 AN: 284

European-Non Finnish (NFE) AF: 0.660 AC: 44611 AN: 67602

Other (OTH) AF: 0.704 AC: 1462 AN: 2078

Alfa AF: 0.677 Hom.: 147694

Bravo AF: 0.734

Asia WGS AF: 0.720 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.37
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: rs6493402; hg19: chr15-50397504;