chr15-50145618-T-C

Variant names:

• chr15-50145618-T-C
• rs12443171
• ENST00000558829.1:c.-43+36643A>G

Variant summary

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

The ENST00000558829.1(ATP8B4):​c.-43+36643A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,078 control chromosomes in the GnomAD database, including 4,587 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 0.23 (4587 hom., cov: 31)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	XM_011522056.4	c.-43+36014A>G		intron_variant	Intron 1 of 28		XP_011520358.3
ATP8B4	XM_017022587.3	c.-43+36014A>G		intron_variant	Intron 1 of 27		XP_016878076.2
ATP8B4	XM_047433096.1	c.-43+36014A>G		intron_variant	Intron 1 of 24		XP_047289052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000558829.1	c.-43+36643A>G		intron_variant	Intron 1 of 3	3		ENSP00000453539.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34902 AN: 151962 Hom.: 4586 Cov.: 31

Gnomad AFR AF: 0.0902

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.230 AC: 34907 AN: 152078 Hom.: 4587 Cov.: 31 AF XY: 0.230 AC XY: 17115 AN XY: 74334

African (AFR) AF: 0.0903 AC: 3749 AN: 41520

American (AMR) AF: 0.228 AC: 3489 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2126 AN: 5154

South Asian (SAS) AF: 0.284 AC: 1368 AN: 4820

European-Finnish (FIN) AF: 0.279 AC: 2954 AN: 10572

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19287 AN: 67946

Other (OTH) AF: 0.251 AC: 529 AN: 2110

Alfa AF: 0.269 Hom.: 7374

Bravo AF: 0.220

Asia WGS AF: 0.291 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.67
PhyloP100		-0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12443171; hg19: chr15-50437815;