12-124800202-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005505.5(SCARB1):c.1050T>C(p.Ala350Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 1,612,832 control chromosomes in the GnomAD database, including 248,441 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005505.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCARB1 | NM_005505.5 | c.1050T>C | p.Ala350Ala | synonymous_variant | Exon 8 of 13 | ENST00000261693.11 | NP_005496.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.627 AC: 95273AN: 151928Hom.: 31181 Cov.: 32
GnomAD3 exomes AF: 0.588 AC: 147686AN: 251150Hom.: 44658 AF XY: 0.576 AC XY: 78145AN XY: 135746
GnomAD4 exome AF: 0.541 AC: 789584AN: 1460786Hom.: 217210 Cov.: 42 AF XY: 0.538 AC XY: 391323AN XY: 726740
GnomAD4 genome AF: 0.627 AC: 95381AN: 152046Hom.: 31231 Cov.: 32 AF XY: 0.630 AC XY: 46829AN XY: 74336
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is associated with the following publications: (PMID: 27651445, 23510561, 28008009, 12519372, 19806217, 17476110, 10397692, 20060115) -
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SCARB1-related disorder Benign:1
This variant is classified as 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