NM_001374385.1:c.3532-15C>T

Variant names:

• chr18-57648727-G-A
• rs12958967
• NM_001374385.1:c.3532-15C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001374385.1(ATP8B1):​c.3532-15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,548,334 control chromosomes in the GnomAD database, including 50,815 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (3745 hom., cov: 32)
  • Exomes 𝑓: 0.25 (47070 hom.)
• Consequence: ATP8B1 NM_001374385.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:8
• Conservation: PhyloP100: 0.271
• Publications: 6 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 18-57648727-G-A is Benign according to our data. Variant chr18-57648727-G-A is described in ClinVar as [Benign]. Clinvar id is 259823.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATP8B1	NM_001374385.1	c.3532-15C>T		intron_variant	Intron 27 of 27	ENST00000648908.2	NP_001361314.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATP8B1	ENST00000648908.2	c.3532-15C>T		intron_variant	Intron 27 of 27		NM_001374385.1	ENSP00000497896.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30028 AN: 151812 Hom.: 3745 Cov.: 32

Gnomad AFR AF: 0.0655

Gnomad AMI AF: 0.0749

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0161

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.228

GnomAD2 exomes AF: 0.217 AC: 32134 AN: 148126 AF XY: 0.221

Gnomad AFR exome AF: 0.0629

Gnomad AMR exome AF: 0.189

Gnomad ASJ exome AF: 0.279

Gnomad EAS exome AF: 0.00963

Gnomad FIN exome AF: 0.277

Gnomad NFE exome AF: 0.270

Gnomad OTH exome AF: 0.244

GnomAD4 exome AF: 0.253 AC: 353833 AN: 1396404 Hom.: 47070 Cov.: 33 AF XY: 0.252 AC XY: 173556 AN XY: 688616

African (AFR) AF: 0.0582 AC: 1834 AN: 31524

American (AMR) AF: 0.193 AC: 6900 AN: 35696

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 6852 AN: 25150

East Asian (EAS) AF: 0.00787 AC: 281 AN: 35722

South Asian (SAS) AF: 0.208 AC: 16457 AN: 79254

European-Finnish (FIN) AF: 0.277 AC: 13569 AN: 48940

Middle Eastern (MID) AF: 0.235 AC: 958 AN: 4074

European-Non Finnish (NFE) AF: 0.272 AC: 293636 AN: 1078232

Other (OTH) AF: 0.231 AC: 13346 AN: 57812

GnomAD4 genome AF: 0.198 AC: 30032 AN: 151930 Hom.: 3745 Cov.: 32 AF XY: 0.196 AC XY: 14542 AN XY: 74252

African (AFR) AF: 0.0655 AC: 2715 AN: 41434

American (AMR) AF: 0.204 AC: 3112 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3462

East Asian (EAS) AF: 0.0161 AC: 83 AN: 5146

South Asian (SAS) AF: 0.193 AC: 932 AN: 4822

European-Finnish (FIN) AF: 0.294 AC: 3112 AN: 10578

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18517 AN: 67906

Other (OTH) AF: 0.224 AC: 474 AN: 2112

Alfa AF: 0.244 Hom.: 19126

Bravo AF: 0.182

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:3

Jan 24, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Feb 25, 2016

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Progressive familial intrahepatic cholestasis type 1 Benign:2

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cholestasis, intrahepatic, of pregnancy, 1 Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.41
PhyloP100		0.27
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: rs12958967; hg19: chr18-55315959;