rs35069772
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_005506.4(SCARB2):c.228C>T(p.Leu76=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,948 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 (★★). Synonymous variant affecting the same amino acid position (i.e. L76L) has been classified as Likely benign.
Frequency
Consequence
NM_005506.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB2 | NM_005506.4 | c.228C>T | p.Leu76= | synonymous_variant | 2/12 | ENST00000264896.8 | |
SCARB2 | NM_001204255.2 | c.228C>T | p.Leu76= | synonymous_variant | 2/9 | ||
SCARB2 | XM_047416429.1 | c.-247C>T | 5_prime_UTR_variant | 2/12 | |||
SCARB2 | XM_047416430.1 | c.-247C>T | 5_prime_UTR_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB2 | ENST00000264896.8 | c.228C>T | p.Leu76= | synonymous_variant | 2/12 | 1 | NM_005506.4 | P4 | |
ENST00000651366.1 | n.103-4212G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251430Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135888
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461728Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727186
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74368
ClinVar
Submissions by phenotype
SCARB2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 15, 2022 | 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). - |
Action myoclonus-renal failure syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 19, 2022 | - - |
Progressive myoclonic epilepsy Benign:1
Likely 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