rs2228380
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005506.4(SCARB2):c.1186G>T(p.Val396Phe) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V396I) has been classified as Benign.
Frequency
Consequence
NM_005506.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCARB2 | NM_005506.4 | c.1186G>T | p.Val396Phe | missense_variant, splice_region_variant | 9/12 | ENST00000264896.8 | |
SCARB2 | NM_001204255.2 | c.757G>T | p.Val253Phe | missense_variant, splice_region_variant | 6/9 | ||
SCARB2 | XM_047416429.1 | c.712G>T | p.Val238Phe | missense_variant, splice_region_variant | 9/12 | ||
SCARB2 | XM_047416430.1 | c.712G>T | p.Val238Phe | missense_variant, splice_region_variant | 9/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCARB2 | ENST00000264896.8 | c.1186G>T | p.Val396Phe | missense_variant, splice_region_variant | 9/12 | 1 | NM_005506.4 | P4 | |
ENST00000651366.1 | n.102+19138C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251368Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135858
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at