rs367657189

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_182895.5(SCARF2):​c.2579G>C​(p.Arg860Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000783 in 1,276,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. 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. R860K) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 7.8e-7 ( 0 hom. )

Consequence

SCARF2
NM_182895.5 missense

Scores

1
1
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.07
Variant links:
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15125886).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCARF2NM_182895.5 linkc.2579G>C p.Arg860Thr missense_variant Exon 11 of 11 ENST00000622235.5 NP_878315.2 Q96GP6-2
SCARF2NM_153334.7 linkc.2594G>C p.Arg865Thr missense_variant Exon 11 of 11 NP_699165.3 Q96GP6-1
SCARF2XM_047441585.1 linkc.2693G>C p.Arg898Thr missense_variant Exon 11 of 11 XP_047297541.1
SCARF2XM_017029065.3 linkc.*808G>C 3_prime_UTR_variant Exon 11 of 11 XP_016884554.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCARF2ENST00000622235.5 linkc.2579G>C p.Arg860Thr missense_variant Exon 11 of 11 1 NM_182895.5 ENSP00000477564.2 Q96GP6-2
SCARF2ENST00000623402.1 linkc.2594G>C p.Arg865Thr missense_variant Exon 11 of 11 1 ENSP00000485276.1 Q96GP6-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.83e-7
AC:
1
AN:
1276408
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
626466
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.80e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
18
DANN
Benign
0.94
Eigen
Benign
-0.68
Eigen_PC
Benign
-0.64
FATHMM_MKL
Benign
0.13
N
LIST_S2
Benign
0.66
T;T
M_CAP
Uncertain
0.12
D
MetaRNN
Benign
0.15
T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Pathogenic
0.80
T
Sift4G
Benign
0.49
T;T
Vest4
0.22
MVP
0.072
ClinPred
0.75
D
GERP RS
3.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.12
gMVP
0.14

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs367657189; hg19: chr22-20779687; API