chr15-49929161-A-C

Variant names:

• chr15-49929161-A-C
• rs2413980
• NM_024837.4:c.1642+1958T>G

Variant summary

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

The NM_024837.4(ATP8B4):​c.1642+1958T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,084 control chromosomes in the GnomAD database, including 1,693 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 0.13 (1693 hom., cov: 33)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.980
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	NM_024837.4	MANE Select	c.1642+1958T>G		intron	N/A	NP_079113.2
	ATP8B4	NR_073596.2		n.1694+4856T>G		intron	N/A
	ATP8B4	NR_073597.2		n.1795+1958T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000284509.11	TSL:5 MANE Select	c.1642+1958T>G		intron	N/A	ENSP00000284509.6
	ATP8B4	ENST00000557955.5	TSL:1	n.1642+1958T>G		intron	N/A	ENSP00000453690.1
	ATP8B4	ENST00000558906.5	TSL:1	n.*1172+4856T>G		intron	N/A	ENSP00000452956.1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19749 AN: 151966 Hom.: 1692 Cov.: 33

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.130 AC: 19757 AN: 152084 Hom.: 1693 Cov.: 33 AF XY: 0.139 AC XY: 10336 AN XY: 74344

African (AFR) AF: 0.0532 AC: 2211 AN: 41534

American (AMR) AF: 0.150 AC: 2282 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1817 AN: 5150

South Asian (SAS) AF: 0.173 AC: 833 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2883 AN: 10576

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9224 AN: 67962

Other (OTH) AF: 0.107 AC: 226 AN: 2106

Alfa AF: 0.132 Hom.: 770

Bravo AF: 0.117

Asia WGS AF: 0.234 AC: 814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.36
PhyloP100		0.98
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: rs2413980; hg19: chr15-50221358;