rs11568366
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_003742.4(ABCB11):āc.3435A>Gā(p.Lys1145=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000146 in 1,613,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.00080 ( 0 hom., cov: 32)
Exomes š: 0.000078 ( 0 hom. )
Consequence
ABCB11
NM_003742.4 synonymous
NM_003742.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.616
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 2-168927339-T-C is Benign according to our data. Variant chr2-168927339-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 283582.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.616 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCB11 | NM_003742.4 | c.3435A>G | p.Lys1145= | synonymous_variant | 26/28 | ENST00000650372.1 | NP_003733.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCB11 | ENST00000650372.1 | c.3435A>G | p.Lys1145= | synonymous_variant | 26/28 | NM_003742.4 | ENSP00000497931 | P1 | ||
ABCB11 | ENST00000649448.1 | c.1812A>G | p.Lys604= | synonymous_variant | 13/15 | ENSP00000497165 | ||||
ABCB11 | ENST00000439188.1 | c.*1882-49A>G | intron_variant, NMD_transcript_variant | 2 | ENSP00000416058 |
Frequencies
GnomAD3 genomes AF: 0.000802 AC: 122AN: 152170Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000217 AC: 54AN: 248996Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135084
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GnomAD4 exome AF: 0.0000780 AC: 114AN: 1461520Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727044
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GnomAD4 genome AF: 0.000801 AC: 122AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.000725 AC XY: 54AN XY: 74476
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 23, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 02, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at