rs11632411

Variant names:

• chr15-50144854-C-A
• rs11632411
• ENST00000558829.1:c.-43+37407G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-50144854-C-A
• chr15-50144854-C-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+37407G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,026 control chromosomes in the GnomAD database, including 2,168 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 0.16 (2168 hom., cov: 31)
• Consequence: ATP8B4 ENST00000558829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721
• 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	XM_011522056.4	c.-43+36778G>T		intron_variant	Intron 1 of 28		XP_011520358.3
ATP8B4	XM_017022587.3	c.-43+36778G>T		intron_variant	Intron 1 of 27		XP_016878076.2
ATP8B4	XM_047433096.1	c.-43+36778G>T		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+37407G>T		intron_variant	Intron 1 of 3	3		ENSP00000453539.1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24514 AN: 151910 Hom.: 2162 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0837

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.161 AC: 24548 AN: 152026 Hom.: 2168 Cov.: 31 AF XY: 0.156 AC XY: 11558 AN XY: 74308

African (AFR) AF: 0.202 AC: 8378 AN: 41458

American (AMR) AF: 0.190 AC: 2902 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3464

East Asian (EAS) AF: 0.0612 AC: 317 AN: 5178

South Asian (SAS) AF: 0.142 AC: 684 AN: 4816

European-Finnish (FIN) AF: 0.0545 AC: 575 AN: 10552

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10383 AN: 67978

Other (OTH) AF: 0.190 AC: 400 AN: 2100

Alfa AF: 0.0726 Hom.: 91

Bravo AF: 0.175

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.9
DANN	Benign	0.83
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs11632411; hg19: chr15-50437051;