12-124782744-T-A
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005505.5(SCARB1):c.1469A>T(p.Tyr490Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,680 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005505.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCARB1 | NM_005505.5 | c.1469A>T | p.Tyr490Phe | missense_variant | Exon 12 of 13 | ENST00000261693.11 | NP_005496.4 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251436 AF XY: 0.00000736 show subpopulations
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460680Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726716 show subpopulations
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1469A>T (p.Y490F) alteration is located in exon 12 (coding exon 12) of the SCARB1 gene. This alteration results from a A to T substitution at nucleotide position 1469, causing the tyrosine (Y) at amino acid position 490 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at