chr15-49975862-G-A

Variant names:

• chr15-49975862-G-A
• rs4143620
• NM_024837.4:c.1035-3072C>T

Variant summary

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

The NM_024837.4(ATP8B4):​c.1035-3072C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 151,896 control chromosomes in the GnomAD database, including 471 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 0.054 (471 hom., cov: 33)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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.1035-3072C>T		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.1276-3072C>T		intron	N/A
	ATP8B4	NR_073597.2		n.1188-3072C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.1035-3072C>T		intron	N/A	ENSP00000284509.6	Q8TF62
	ATP8B4	ENST00000557955.5	TSL:1	n.1035-3072C>T		intron	N/A	ENSP00000453690.1	H0YMP8
	ATP8B4	ENST00000558906.5	TSL:1	n.*754-3072C>T		intron	N/A	ENSP00000452956.1	H0YLJ1

Frequencies

GnomAD3 genomes AF: 0.0542 AC: 8233 AN: 151778 Hom.: 470 Cov.: 33

Gnomad AFR AF: 0.0120

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0942

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0542 AC: 8235 AN: 151896 Hom.: 471 Cov.: 33 AF XY: 0.0593 AC XY: 4405 AN XY: 74230

African (AFR) AF: 0.0119 AC: 495 AN: 41446

American (AMR) AF: 0.0946 AC: 1442 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1485 AN: 5150

South Asian (SAS) AF: 0.0726 AC: 348 AN: 4796

European-Finnish (FIN) AF: 0.0938 AC: 989 AN: 10540

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0483 AC: 3284 AN: 67944

Other (OTH) AF: 0.0440 AC: 93 AN: 2112

Alfa AF: 0.0512 Hom.: 28

Bravo AF: 0.0515

Asia WGS AF: 0.154 AC: 533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.5
DANN	Benign	0.71
PhyloP100		-0.80
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: rs4143620; hg19: chr15-50268059;