rs143655258
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005506.4(SCARB2):āc.475A>Gā(p.Met159Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00924 in 1,614,106 control chromosomes in the GnomAD database, including 98 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 Benign (ā ā ).
Frequency
Consequence
NM_005506.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB2 | NM_005506.4 | c.475A>G | p.Met159Val | missense_variant | 4/12 | ENST00000264896.8 | |
SCARB2 | XM_047416429.1 | c.1A>G | p.Met1? | start_lost | 4/12 | ||
SCARB2 | XM_047416430.1 | c.1A>G | p.Met1? | start_lost | 4/12 | ||
SCARB2 | NM_001204255.2 | c.276-3744A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB2 | ENST00000264896.8 | c.475A>G | p.Met159Val | missense_variant | 4/12 | 1 | NM_005506.4 | P4 | |
ENST00000651366.1 | n.103-20312T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00837 AC: 1274AN: 152218Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00861 AC: 2163AN: 251304Hom.: 18 AF XY: 0.00872 AC XY: 1185AN XY: 135822
GnomAD4 exome AF: 0.00933 AC: 13636AN: 1461770Hom.: 90 Cov.: 31 AF XY: 0.00936 AC XY: 6810AN XY: 727186
GnomAD4 genome ? AF: 0.00836 AC: 1273AN: 152336Hom.: 8 Cov.: 33 AF XY: 0.00824 AC XY: 614AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2014 | 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. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 03, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | ENSG00000286074: BS1, BS2; SCARB2: BP4, BS1, BS2 - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2017 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Action myoclonus-renal failure syndrome Benign:1
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Focal segmental glomerulosclerosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Oct 13, 2021 | - - |
Progressive myoclonic epilepsy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at