rs4494483

Variant names:

• chr15-49860077-T-A
• rs4494483
• ENST00000557955.5:n.*1394A>T

Your query was ambiguous. Multiple possible variants found:

• chr15-49860077-T-A
• chr15-49860077-T-G

Variant summary

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

The ENST00000557955.5(ATP8B4):​n.*1394A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,285,546 control chromosomes in the GnomAD database, including 46,394 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 0.26 (5172 hom., cov: 32)
  • Exomes 𝑓: 0.26 (41222 hom.)
• Consequence: ATP8B4 ENST00000557955.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.*117A>T		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	ENST00000284509.11	c.*117A>T		3_prime_UTR_variant	Exon 28 of 28	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38777 AN: 151984 Hom.: 5163 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.259

GnomAD4 exome AF: 0.263 AC: 298421 AN: 1133444 Hom.: 41222 Cov.: 16 AF XY: 0.263 AC XY: 148774 AN XY: 565446

African (AFR) AF: 0.262 AC: 6726 AN: 25688

American (AMR) AF: 0.155 AC: 4447 AN: 28610

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 4610 AN: 18720

East Asian (EAS) AF: 0.0224 AC: 845 AN: 37768

South Asian (SAS) AF: 0.238 AC: 15233 AN: 63962

European-Finnish (FIN) AF: 0.268 AC: 10189 AN: 38062

Middle Eastern (MID) AF: 0.296 AC: 1443 AN: 4870

European-Non Finnish (NFE) AF: 0.279 AC: 242250 AN: 866930

Other (OTH) AF: 0.260 AC: 12678 AN: 48834

GnomAD4 genome AF: 0.255 AC: 38811 AN: 152102 Hom.: 5172 Cov.: 32 AF XY: 0.250 AC XY: 18618 AN XY: 74362

African (AFR) AF: 0.262 AC: 10874 AN: 41478

American (AMR) AF: 0.214 AC: 3266 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3472

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5182

South Asian (SAS) AF: 0.230 AC: 1106 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2687 AN: 10572

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18891 AN: 67986

Other (OTH) AF: 0.256 AC: 540 AN: 2112

Alfa AF: 0.264 Hom.: 695

Bravo AF: 0.249

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.075
DANN	Benign	0.82
PhyloP100		-2.7
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: rs4494483; hg19: chr15-50152274;