18-57646472-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001374385.1(ATP8B1):c.*2015del variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.168 in 152,484 control chromosomes in the GnomAD database, including 2,325 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2320 hom., cov: 29)
  • Exomes 𝑓: 0.16 (5 hom.)
• Consequence: ATP8B1 NM_001374385.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.89

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 -10 ACMG points.

• BP6: Variant 18-57646472-AT-A is Benign according to our data. Variant chr18-57646472-AT-A is described in ClinVar as [Benign]. Clinvar id is 327438.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ATP8B1	NM_001374385.1	c.*2015del		3_prime_UTR_variant	28/28	ENST00000648908.2
ATP8B1-AS1	NR_164148.1	n.682+4427del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATP8B1	ENST00000648908.2	c.*2015del		3_prime_UTR_variant	28/28		NM_001374385.1	P1
	ENST00000588925.5	n.570+4427del		intron_variant, non_coding_transcript_variant		2
ATP8B1-AS1	ENST00000592201.1	n.663+4427del		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25499 AN: 152012 Hom.: 2314 Cov.: 29

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.161 AC: 57 AN: 354 Hom.: 5 Cov.: 0 AF XY: 0.189 AC XY: 40 AN XY: 212

Gnomad4 FIN exome AF: 0.163

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.168 AC: 25520 AN: 152130 Hom.: 2320 Cov.: 29 AF XY: 0.168 AC XY: 12487 AN XY: 74378

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0755 Hom.: 99

Bravo AF: 0.169

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Progressive familial intrahepatic cholestasis Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs35833803; hg19: chr18-55313704;