22-20425438-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_182895.5(SCARF2):c.2538G>A(p.Pro846Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000785 in 1,427,030 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 (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000080 ( 0 hom. )
Consequence
SCARF2
NM_182895.5 synonymous
NM_182895.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.898
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 22-20425438-C-T is Benign according to our data. Variant chr22-20425438-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2176744.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.898 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCARF2 | NM_182895.5 | c.2538G>A | p.Pro846Pro | synonymous_variant | Exon 11 of 11 | ENST00000622235.5 | NP_878315.2 | |
SCARF2 | NM_153334.7 | c.2553G>A | p.Pro851Pro | synonymous_variant | Exon 11 of 11 | NP_699165.3 | ||
SCARF2 | XM_047441585.1 | c.2652G>A | p.Pro884Pro | synonymous_variant | Exon 11 of 11 | XP_047297541.1 | ||
SCARF2 | XM_017029065.3 | c.*767G>A | 3_prime_UTR_variant | Exon 11 of 11 | XP_016884554.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SCARF2 | ENST00000622235.5 | c.2538G>A | p.Pro846Pro | synonymous_variant | Exon 11 of 11 | 1 | NM_182895.5 | ENSP00000477564.2 | ||
SCARF2 | ENST00000623402.1 | c.2553G>A | p.Pro851Pro | synonymous_variant | Exon 11 of 11 | 1 | ENSP00000485276.1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152090Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000752 AC: 9AN: 119750Hom.: 0 AF XY: 0.000115 AC XY: 8AN XY: 69772
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GnomAD4 exome AF: 0.0000800 AC: 102AN: 1274832Hom.: 0 Cov.: 31 AF XY: 0.0000814 AC XY: 51AN XY: 626232
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74416
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Nov 03, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at