15-50137986-G-T

Variant names:

• chr15-50137986-G-T
• rs7342574
• ENST00000895127.1:c.-42-30978C>A

Variant summary

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

The ENST00000558829.1(ATP8B4):​c.-42-30978C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,064 control chromosomes in the GnomAD database, including 8,111 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 0.31 (8111 hom., cov: 32)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.10
• Publications: 1 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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558829.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B4	ENST00000895127.1		c.-42-30978C>A		intron	N/A	ENSP00000565186.1
	ATP8B4	ENST00000966552.1		c.-42-30978C>A		intron	N/A	ENSP00000636611.1
	ATP8B4	ENST00000558829.1	TSL:3	c.-42-30978C>A		intron	N/A	ENSP00000453539.1	H0YMB5

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47298 AN: 151948 Hom.: 8102 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.311 AC: 47353 AN: 152064 Hom.: 8111 Cov.: 32 AF XY: 0.317 AC XY: 23527 AN XY: 74304

African (AFR) AF: 0.432 AC: 17930 AN: 41482

American (AMR) AF: 0.320 AC: 4895 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3466

East Asian (EAS) AF: 0.486 AC: 2510 AN: 5164

South Asian (SAS) AF: 0.371 AC: 1784 AN: 4810

European-Finnish (FIN) AF: 0.283 AC: 2988 AN: 10564

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15889 AN: 67982

Other (OTH) AF: 0.273 AC: 576 AN: 2108

Alfa AF: 0.288 Hom.: 2250

Bravo AF: 0.322

Asia WGS AF: 0.471 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.6
DANN	Benign	0.79
PhyloP100		3.1

Splicing

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

Other links and lift over

dbSNP: rs7342574; hg19: chr15-50430183;