chr7-87509343-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001348946.2(ABCB1):c.3421T>A(p.Ser1141Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00332 in 1,614,076 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001348946.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB1 | NM_001348946.2 | c.3421T>A | p.Ser1141Thr | missense_variant | 26/28 | ENST00000622132.5 | |
ABCB1 | NM_001348945.2 | c.3631T>A | p.Ser1211Thr | missense_variant | 30/32 | ||
ABCB1 | NM_000927.5 | c.3421T>A | p.Ser1141Thr | missense_variant | 27/29 | ||
ABCB1 | NM_001348944.2 | c.3421T>A | p.Ser1141Thr | missense_variant | 28/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB1 | ENST00000622132.5 | c.3421T>A | p.Ser1141Thr | missense_variant | 26/28 | 1 | NM_001348946.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0180 AC: 2738AN: 152122Hom.: 71 Cov.: 32
GnomAD3 exomes AF: 0.00468 AC: 1176AN: 251304Hom.: 34 AF XY: 0.00341 AC XY: 463AN XY: 135810
GnomAD4 exome AF: 0.00178 AC: 2602AN: 1461836Hom.: 83 Cov.: 35 AF XY: 0.00149 AC XY: 1084AN XY: 727216
GnomAD4 genome AF: 0.0181 AC: 2754AN: 152240Hom.: 72 Cov.: 32 AF XY: 0.0169 AC XY: 1259AN XY: 74452
ClinVar
Submissions by phenotype
ABCB1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 24, 2020 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at