rs2009833

Variant names:

• chr15-49901356-G-A
• rs2009833
• NM_024837.4:c.2142-117C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-49901356-G-A
• chr15-49901356-G-C
• chr15-49901356-G-T

Variant summary

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

The NM_024837.4(ATP8B4):​c.2142-117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 1,084,428 control chromosomes in the GnomAD database, including 94,047 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 0.40 (13255 hom., cov: 33)
  • Exomes 𝑓: 0.40 (80792 hom.)
• Consequence: ATP8B4 NM_024837.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 8 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=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B4	NM_024837.4	c.2142-117C>T		intron_variant	Intron 20 of 27	ENST00000284509.11	NP_079113.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B4	ENST00000284509.11	c.2142-117C>T		intron_variant	Intron 20 of 27	5	NM_024837.4	ENSP00000284509.6

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61141 AN: 151932 Hom.: 13247 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.423

GnomAD4 exome AF: 0.401 AC: 373874 AN: 932378 Hom.: 80792 AF XY: 0.403 AC XY: 187740 AN XY: 465774

African (AFR) AF: 0.310 AC: 6503 AN: 21004

American (AMR) AF: 0.578 AC: 11738 AN: 20318

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 5286 AN: 16712

East Asian (EAS) AF: 0.880 AC: 29317 AN: 33332

South Asian (SAS) AF: 0.492 AC: 25694 AN: 52212

European-Finnish (FIN) AF: 0.463 AC: 17099 AN: 36912

Middle Eastern (MID) AF: 0.286 AC: 955 AN: 3344

European-Non Finnish (NFE) AF: 0.368 AC: 260267 AN: 706756

Other (OTH) AF: 0.407 AC: 17015 AN: 41788

GnomAD4 genome AF: 0.402 AC: 61190 AN: 152050 Hom.: 13255 Cov.: 33 AF XY: 0.412 AC XY: 30631 AN XY: 74296

African (AFR) AF: 0.322 AC: 13347 AN: 41484

American (AMR) AF: 0.526 AC: 8031 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1053 AN: 3470

East Asian (EAS) AF: 0.857 AC: 4436 AN: 5178

South Asian (SAS) AF: 0.498 AC: 2399 AN: 4822

European-Finnish (FIN) AF: 0.477 AC: 5019 AN: 10530

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25576 AN: 67968

Other (OTH) AF: 0.424 AC: 897 AN: 2114

Alfa AF: 0.375 Hom.: 21777

Bravo AF: 0.400

Asia WGS AF: 0.649 AC: 2252 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
DANN	Benign	0.66
PhyloP100		1.4
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: rs2009833; hg19: chr15-50193553; COSMIC: COSV52719446; COSMIC: COSV52719446;