22-20425438-C-T

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

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.898
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]

Genome browser will be placed here

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
SCARF2NM_182895.5 linkc.2538G>A p.Pro846Pro synonymous_variant Exon 11 of 11 ENST00000622235.5 NP_878315.2 Q96GP6-2
SCARF2NM_153334.7 linkc.2553G>A p.Pro851Pro synonymous_variant Exon 11 of 11 NP_699165.3 Q96GP6-1
SCARF2XM_047441585.1 linkc.2652G>A p.Pro884Pro synonymous_variant Exon 11 of 11 XP_047297541.1
SCARF2XM_017029065.3 linkc.*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
SCARF2ENST00000622235.5 linkc.2538G>A p.Pro846Pro synonymous_variant Exon 11 of 11 1 NM_182895.5 ENSP00000477564.2 Q96GP6-2
SCARF2ENST00000623402.1 linkc.2553G>A p.Pro851Pro synonymous_variant Exon 11 of 11 1 ENSP00000485276.1 Q96GP6-1

Frequencies

GnomAD3 genomes
AF:
0.0000658
AC:
10
AN:
152090
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.0000752
AC:
9
AN:
119750
Hom.:
0
AF XY:
0.000115
AC XY:
8
AN XY:
69772
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000153
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000800
AC:
102
AN:
1274832
Hom.:
0
Cov.:
31
AF XY:
0.0000814
AC XY:
51
AN XY:
626232
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000309
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000157
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000823
Gnomad4 OTH exome
AF:
0.000155
GnomAD4 genome
AF:
0.0000657
AC:
10
AN:
152198
Hom.:
0
Cov.:
33
AF XY:
0.0000672
AC XY:
5
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00142
Bravo
AF:
0.0000982

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

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
9.2
DANN
Benign
0.87
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs758888141; hg19: chr22-20779728; API