rs1893673

chr18-57660068-T-Cchr18-57660068-T-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B1	NM_001374385.1	c.2707+1106A>G		intron_variant		ENST00000648908.2
ATP8B1-AS1	NR_164148.1	n.683-7938T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B1	ENST00000648908.2	c.2707+1106A>G		intron_variant			NM_001374385.1	P1
	ENST00000588925.5	n.570+18016T>C		intron_variant, non_coding_transcript_variant		2
ATP8B1-AS1	ENST00000592201.1	n.664-7938T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.474

Alfa AF: 0.470 Hom.: 34401

Bravo AF: 0.451

Asia WGS AF: 0.470 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.78
Dann	Benign	0.27

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

Publications

LitVar

Other links and lift over

dbSNP: rs1893673; hg19: chr18-55327300;