rs5844420

chr22-20425735-G-GC

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 6P and 12B. PVS1_Strong PM2 BP6_Very_Strong BS2

The NM_182895.5(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 NM_182895.5 frameshift
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• 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]

ACMG classification

Verdict is Likely_benign. Variant got -6 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.
• BS2: High Homozygotes in GnomAdExome at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCARF2	NM_182895.5	c.2240_2241insG	p.Gly749ArgfsTer25	frameshift_variant	11/11	ENST00000622235.5
SCARF2	NM_153334.7	c.2255_2256insG	p.Gly754ArgfsTer25	frameshift_variant	11/11
SCARF2	XM_047441585.1	c.2354_2355insG	p.Gly787ArgfsTer25	frameshift_variant	11/11
SCARF2	XM_017029065.3	c.*469_*470insG		3_prime_UTR_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCARF2	ENST00000622235.5	c.2240_2241insG	p.Gly749ArgfsTer25	frameshift_variant	11/11	1	NM_182895.5	P1
SCARF2	ENST00000623402.1	c.2255_2256insG	p.Gly754ArgfsTer25	frameshift_variant	11/11	1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 1.00 AC: 12 AN: 12 Hom.: 6 AF XY: 1.00 AC XY: 4 AN XY: 4

Gnomad NFE exome AF: 1.00

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

Alfa AF: 1.00 Hom.: 2224

Asia WGS AF: 0.998 AC: 3111 AN: 3116

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
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% -

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs5844420; hg19: chr22-20780024;