rs5844420
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 6P and 8B. PVS1_StrongPM2BP6_Very_Strong
The ENST00000622235.5(SCARF2):c.2240_2241insG(p.Gly749ArgfsTer25) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: not found (cov: 32)
Consequence
SCARF2
ENST00000622235.5 frameshift
ENST00000622235.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.399
Genes affected
SCARF2 (HGNC:19869): (scavenger receptor class F member 2) The protein encoded by this gene is similar to SCARF1/SREC-I, a scavenger receptor protein that mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). This protein has only little activity of internalizing modified low density lipoproteins (LDL), but it can interact with SCARF1 through its extracellular domain. The association of this protein with SCARF1 is suppressed by the presence of scavenger ligands. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.139 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 22-20425735-G-GC is Benign according to our data. Variant chr22-20425735-G-GC is described in ClinVar as [Benign]. Clinvar id is 403414.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCARF2 | NM_182895.5 | c.2240_2241insG | p.Gly749ArgfsTer25 | frameshift_variant | 11/11 | ENST00000622235.5 | NP_878315.2 | |
SCARF2 | NM_153334.7 | c.2255_2256insG | p.Gly754ArgfsTer25 | frameshift_variant | 11/11 | NP_699165.3 | ||
SCARF2 | XM_047441585.1 | c.2354_2355insG | p.Gly787ArgfsTer25 | frameshift_variant | 11/11 | XP_047297541.1 | ||
SCARF2 | XM_017029065.3 | c.*469_*470insG | 3_prime_UTR_variant | 11/11 | XP_016884554.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCARF2 | ENST00000622235.5 | c.2240_2241insG | p.Gly749ArgfsTer25 | frameshift_variant | 11/11 | 1 | NM_182895.5 | ENSP00000477564 | P1 | |
SCARF2 | ENST00000623402.1 | c.2255_2256insG | p.Gly754ArgfsTer25 | frameshift_variant | 11/11 | 1 | ENSP00000485276 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 1.00 AC: 12AN: 12Hom.: 6 AF XY: 1.00 AC XY: 4AN XY: 4
GnomAD3 exomes
AF:
AC:
12
AN:
12
Hom.:
AF XY:
AC XY:
4
AN XY:
4
Gnomad NFE exome
AF:
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
3111
AN:
3116
ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes: 2105/2178=96.64% - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at