rs1893673

Variant names:

• chr18-57660068-T-C
• rs1893673
• NM_001374385.1:c.2707+1106A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-57660068-T-C
• chr18-57660068-T-G

Variant summary

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

The NM_001374385.1(ATP8B1):​c.2707+1106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,918 control chromosomes in the GnomAD database, including 16,225 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 0.46 (16225 hom., cov: 31)
• Consequence: ATP8B1 NM_001374385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001374385.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B1	NM_001374385.1	MANE Select	c.2707+1106A>G		intron	N/A	NP_001361314.1	O43520
	ATP8B1	NM_005603.6		c.2707+1106A>G		intron	N/A	NP_005594.2	O43520
	ATP8B1	NM_001374386.1		c.2557+1106A>G		intron	N/A	NP_001361315.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ATP8B1	ENST00000648908.2	MANE Select	c.2707+1106A>G		intron	N/A	ENSP00000497896.1	O43520
	ATP8B1-AS1	ENST00000592201.2	TSL:1	n.723-7938T>C		intron	N/A
	ATP8B1	ENST00000857621.1		c.2707+1106A>G		intron	N/A	ENSP00000527680.1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69322 AN: 151800 Hom.: 16215 Cov.: 31

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.457 AC: 69372 AN: 151918 Hom.: 16225 Cov.: 31 AF XY: 0.461 AC XY: 34193 AN XY: 74242

African (AFR) AF: 0.374 AC: 15508 AN: 41420

American (AMR) AF: 0.506 AC: 7717 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1596 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2671 AN: 5166

South Asian (SAS) AF: 0.439 AC: 2112 AN: 4812

European-Finnish (FIN) AF: 0.557 AC: 5868 AN: 10538

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32275 AN: 67942

Other (OTH) AF: 0.474 AC: 1001 AN: 2112

Alfa AF: 0.467 Hom.: 52131

Bravo AF: 0.451

Asia WGS AF: 0.470 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.78
DANN	Benign	0.27
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1893673; hg19: chr18-55327300;