rs319448

Variant names:

• chr18-57692916-G-A
• rs319448
• NM_001374385.1:c.1030-919C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-57692916-G-A
• chr18-57692916-G-T

Variant summary

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

The NM_001374385.1(ATP8B1):​c.1030-919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,014 control chromosomes in the GnomAD database, including 22,382 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 0.52 (22382 hom., cov: 32)
• Consequence: ATP8B1 NM_001374385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256
• Publications: 4 publications found

Genes affected

ATP8B1 (HGNC:3706): (ATPase phospholipid transporting 8B1) This gene encodes a member of the P-type cation transport ATPase family, which belongs to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. Mutations in this gene may result in progressive familial intrahepatic cholestasis type 1 and in benign recurrent intrahepatic cholestasis. [provided by RefSeq, Jul 2008]

ATP8B1-AS1 (HGNC:56042): (ATP8B1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B1	NM_001374385.1	c.1030-919C>T		intron_variant	Intron 11 of 27	ENST00000648908.2	NP_001361314.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B1	ENST00000648908.2	c.1030-919C>T		intron_variant	Intron 11 of 27		NM_001374385.1	ENSP00000497896.1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79200 AN: 151896 Hom.: 22363 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.521 AC: 79251 AN: 152014 Hom.: 22382 Cov.: 32 AF XY: 0.519 AC XY: 38539 AN XY: 74284

African (AFR) AF: 0.291 AC: 12050 AN: 41450

American (AMR) AF: 0.633 AC: 9668 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2231 AN: 3470

East Asian (EAS) AF: 0.685 AC: 3542 AN: 5174

South Asian (SAS) AF: 0.469 AC: 2260 AN: 4822

European-Finnish (FIN) AF: 0.547 AC: 5757 AN: 10530

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.617 AC: 41936 AN: 67986

Other (OTH) AF: 0.561 AC: 1185 AN: 2112

Alfa AF: 0.599 Hom.: 43909

Bravo AF: 0.524

Asia WGS AF: 0.543 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.26
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: rs319448; hg19: chr18-55360148;