chr22-20429630-TCA-T
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_182895.5(SCARF2):c.1328_1329delTG(p.Val443AspfsTer78) variant causes a frameshift change. The variant allele was found at a frequency of 0.000000684 in 1,461,524 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
SCARF2
NM_182895.5 frameshift
NM_182895.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.92
Publications
2 publications found
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]
SCARF2 Gene-Disease associations (from GenCC):
- van den Ende-Gupta syndromeInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 22-20429630-TCA-T is Pathogenic according to our data. Variant chr22-20429630-TCA-T is described in ClinVar as Pathogenic. ClinVar VariationId is 31047.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_182895.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SCARF2 | NM_182895.5 | MANE Select | c.1328_1329delTG | p.Val443AspfsTer78 | frameshift | Exon 8 of 11 | NP_878315.2 | ||
| SCARF2 | NM_153334.7 | c.1328_1329delTG | p.Val443AspfsTer83 | frameshift | Exon 8 of 11 | NP_699165.3 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SCARF2 | ENST00000622235.5 | TSL:1 MANE Select | c.1328_1329delTG | p.Val443AspfsTer78 | frameshift | Exon 8 of 11 | ENSP00000477564.2 | ||
| SCARF2 | ENST00000623402.1 | TSL:1 | c.1328_1329delTG | p.Val443AspfsTer83 | frameshift | Exon 8 of 11 | ENSP00000485276.1 | ||
| ENSG00000277971 | ENST00000429594.1 | TSL:5 | n.*237_*238delTG | non_coding_transcript_exon | Exon 4 of 5 | ENSP00000392268.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461524Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 727106 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461524
Hom.:
AF XY:
AC XY:
0
AN XY:
727106
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33476
American (AMR)
AF:
AC:
0
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26126
East Asian (EAS)
AF:
AC:
0
AN:
39692
South Asian (SAS)
AF:
AC:
0
AN:
86256
European-Finnish (FIN)
AF:
AC:
0
AN:
53196
Middle Eastern (MID)
AF:
AC:
1
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111904
Other (OTH)
AF:
AC:
0
AN:
60384
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
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2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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10
<30
30-35
35-40
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions as Germline
Significance:Pathogenic
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
1
-
-
not provided (1)
1
-
-
Van den Ende-Gupta syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
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
Publications
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