rs16963311

Variant names:

• chr15-50112978-T-C
• rs16963311
• NM_024837.4:c.-42-5970A>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.-42-5970A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,118 control chromosomes in the GnomAD database, including 1,317 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 0.11 (1317 hom., cov: 31)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.-42-5970A>G		intron_variant	Intron 1 of 27	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.-42-5970A>G		intron_variant	Intron 1 of 27	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16414 AN: 152000 Hom.: 1314 Cov.: 31

Gnomad AFR AF: 0.0243

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.108 AC: 16432 AN: 152118 Hom.: 1317 Cov.: 31 AF XY: 0.116 AC XY: 8647 AN XY: 74370

African (AFR) AF: 0.0242 AC: 1005 AN: 41534

American (AMR) AF: 0.100 AC: 1531 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1261 AN: 5144

South Asian (SAS) AF: 0.103 AC: 495 AN: 4822

European-Finnish (FIN) AF: 0.280 AC: 2957 AN: 10576

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8698 AN: 67968

Other (OTH) AF: 0.101 AC: 214 AN: 2112

Alfa AF: 0.114 Hom.: 2181

Bravo AF: 0.0932

Asia WGS AF: 0.140 AC: 486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.81
PhyloP100		-0.79
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: rs16963311; hg19: chr15-50405175;