chr7-87531302-A-C
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM5BP4_StrongBP6_Very_StrongBA1
The NM_001348946.2(ABCB1):āc.2677T>Gā(p.Ser893Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 1,611,172 control chromosomes in the GnomAD database, including 250,710 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S893Y) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001348946.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB1 | NM_001348946.2 | c.2677T>G | p.Ser893Ala | missense_variant | 21/28 | ENST00000622132.5 | |
ABCB1 | NM_001348945.2 | c.2887T>G | p.Ser963Ala | missense_variant | 25/32 | ||
ABCB1 | NM_000927.5 | c.2677T>G | p.Ser893Ala | missense_variant | 22/29 | ||
ABCB1 | NM_001348944.2 | c.2677T>G | p.Ser893Ala | missense_variant | 23/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB1 | ENST00000622132.5 | c.2677T>G | p.Ser893Ala | missense_variant | 21/28 | 1 | NM_001348946.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.641 AC: 97433AN: 151960Hom.: 33483 Cov.: 32
GnomAD3 exomes AF: 0.539 AC: 135082AN: 250640Hom.: 38434 AF XY: 0.524 AC XY: 70967AN XY: 135446
GnomAD4 exome AF: 0.539 AC: 786633AN: 1459094Hom.: 217160 Cov.: 36 AF XY: 0.532 AC XY: 386422AN XY: 725932
GnomAD4 genome ? AF: 0.642 AC: 97571AN: 152078Hom.: 33550 Cov.: 32 AF XY: 0.634 AC XY: 47095AN XY: 74338
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 27, 2014 | - - |
ABCB1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 21, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 13, 2018 | 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. - |
Inflammatory bowel disease 13 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Dec 01, 2003 | - - |
Tramadol response Other:1
drug response, no assertion criteria provided | research | Bruce Budowle Laboratory, University of North Texas Health Science Center | Apr 28, 2018 | - T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1 |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at