rs758857853
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005506.4(SCARB2):c.1087C>A(p.His363Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Synonymous variant affecting the same amino acid position (i.e. H363H) has been classified as Likely benign.
Frequency
Consequence
NM_005506.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB2 | NM_005506.4 | c.1087C>A | p.His363Asn | missense_variant | 8/12 | ENST00000264896.8 | |
SCARB2 | NM_001204255.2 | c.658C>A | p.His220Asn | missense_variant | 5/9 | ||
SCARB2 | XM_047416429.1 | c.613C>A | p.His205Asn | missense_variant | 8/12 | ||
SCARB2 | XM_047416430.1 | c.613C>A | p.His205Asn | missense_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB2 | ENST00000264896.8 | c.1087C>A | p.His363Asn | missense_variant | 8/12 | 1 | NM_005506.4 | P4 | |
ENST00000651366.1 | n.102+20627G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251298Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135794
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461348Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727000
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Action myoclonus-renal failure syndrome Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at