chr2-168923202-T-C

Variant names:

• chr2-168923202-T-C
• rs496550
• NM_003742.4:c.*420A>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_003742.4(ABCB11):​c.*420A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 175,774 control chromosomes in the GnomAD database, including 22,115 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.48 (18879 hom., cov: 32)
  • Exomes 𝑓: 0.50 (3236 hom.)
• Consequence: ABCB11 NM_003742.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.236

Genes affected

ABCB11 (HGNC:42): (ATP binding cassette subfamily B member 11) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. The protein encoded by this gene is the major canalicular bile salt export pump in man. Mutations in this gene cause a form of progressive familial intrahepatic cholestases which are a group of inherited disorders with severe cholestatic liver disease from early infancy. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 2-168923202-T-C is Benign according to our data. Variant chr2-168923202-T-C is described in ClinVar as [Benign]. Clinvar id is 332013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB11	NM_003742.4	c.*420A>G		3_prime_UTR_variant	Exon 28 of 28	ENST00000650372.1	NP_003733.2
ABCB11	XM_011512078.3	c.*374A>G		3_prime_UTR_variant	Exon 29 of 29		XP_011510380.1
ABCB11	XM_017005165.2	c.3867+1455A>G		intron_variant	Intron 27 of 27		XP_016860654.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB11	ENST00000650372	c.*420A>G		3_prime_UTR_variant	Exon 28 of 28		NM_003742.4	ENSP00000497931.1
ABCB11	ENST00000649448	c.*420A>G		3_prime_UTR_variant	Exon 15 of 15			ENSP00000497165.1
ABCB11	ENST00000648875.1	c.225+1455A>G		intron_variant	Intron 2 of 2			ENSP00000497252.1
ABCB11	ENST00000439188.1	n.*2784A>G		downstream_gene_variant		2		ENSP00000416058.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73358 AN: 151866 Hom.: 18880 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.512

GnomAD4 exome AF: 0.505 AC: 12005 AN: 23790 Hom.: 3236 Cov.: 0 AF XY: 0.511 AC XY: 6275 AN XY: 12274

Gnomad4 AFR exome AF: 0.249

Gnomad4 AMR exome AF: 0.544

Gnomad4 ASJ exome AF: 0.630

Gnomad4 EAS exome AF: 0.541

Gnomad4 SAS exome AF: 0.612

Gnomad4 FIN exome AF: 0.470

Gnomad4 NFE exome AF: 0.496

Gnomad4 OTH exome AF: 0.497

GnomAD4 genome AF: 0.483 AC: 73380 AN: 151984 Hom.: 18879 Cov.: 32 AF XY: 0.490 AC XY: 36396 AN XY: 74282

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.560

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.507

Alfa AF: 0.531 Hom.: 30448

Bravo AF: 0.470

Asia WGS AF: 0.605 AC: 2102 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Progressive familial intrahepatic cholestasis type 2 Benign:1

Jan 13, 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.30

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: rs496550; hg19: chr2-169779712; COSMIC: COSV55595495; COSMIC: COSV55595495;