15-49859993-C-T

Variant names:

• chr15-49859993-C-T
• rs4544192
• NM_024837.4:c.*201G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024837.4(ATP8B4):​c.*201G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 557,848 control chromosomes in the GnomAD database, including 19,059 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 0.25 (5114 hom., cov: 32)
  • Exomes 𝑓: 0.25 (13945 hom.)
• Consequence: ATP8B4 NM_024837.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.*201G>A		3_prime_UTR_variant	Exon 28 of 28	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509	c.*201G>A		3_prime_UTR_variant	Exon 28 of 28	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38593 AN: 151584 Hom.: 5105 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.260

GnomAD4 exome AF: 0.248 AC: 100772 AN: 406154 Hom.: 13945 Cov.: 6 AF XY: 0.248 AC XY: 51587 AN XY: 208036

Gnomad4 AFR exome AF: 0.255

Gnomad4 AMR exome AF: 0.178

Gnomad4 ASJ exome AF: 0.243

Gnomad4 EAS exome AF: 0.0165

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.267

Gnomad4 NFE exome AF: 0.273

Gnomad4 OTH exome AF: 0.253

GnomAD4 genome AF: 0.255 AC: 38628 AN: 151694 Hom.: 5114 Cov.: 32 AF XY: 0.250 AC XY: 18502 AN XY: 74070

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.0412

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.256

Alfa AF: 0.260 Hom.: 8827

Bravo AF: 0.249

Asia WGS AF: 0.121 AC: 423 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs4544192; hg19: chr15-50152190;