22-20425532-G-C

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_182895.5(SCARF2):c.2444C>G(p.Ala815Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 1,341,348 control chromosomes in the GnomAD database, including 83,597 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 8753 hom., cov: 32)

Exomes 𝑓: 0.35 ( 74844 hom. )

Consequence

SCARF2
NM_182895.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.751

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]

SCARF2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.164644E-4).

BP6

Variant 22-20425532-G-C is Benign according to our data. Variant chr22-20425532-G-C is described in ClinVar as [Benign]. Clinvar id is 518325.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-20425532-G-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCARF2	NM_182895.5 link	c.2444C>G	p.Ala815Gly	missense_variant	Exon 11 of 11	ENST00000622235.5	NP_878315.2	Q96GP6-2
SCARF2	NM_153334.7 link	c.2459C>G	p.Ala820Gly	missense_variant	Exon 11 of 11		NP_699165.3	Q96GP6-1
SCARF2	XM_047441585.1 link	c.2558C>G	p.Ala853Gly	missense_variant	Exon 11 of 11		XP_047297541.1
SCARF2	XM_017029065.3 link	c.*673C>G		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 link	c.2444C>G	p.Ala815Gly	missense_variant	Exon 11 of 11	1	NM_182895.5	ENSP00000477564.2		Q96GP6-2
SCARF2	ENST00000623402.1 link	c.2459C>G	p.Ala820Gly	missense_variant	Exon 11 of 11	1		ENSP00000485276.1		Q96GP6-1

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50301

AN:

151642

Hom.:

8755

Cov.:

show subpopulations

Gnomad AFR

AF:

0.325

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.359

Gnomad EAS

AF:

0.0585

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.299

Gnomad NFE

AF:

0.366

Gnomad OTH

AF:

0.313

GnomAD3 exomes

AF:

0.301

AC:

7826

AN:

25994

Hom.:

1184

AF XY:

0.309

AC XY:

4775

AN XY:

15464

show subpopulations

Gnomad AFR exome

AF:

0.312

Gnomad AMR exome

AF:

0.150

Gnomad ASJ exome

AF:

0.371

Gnomad EAS exome

AF:

0.0733

Gnomad SAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.412

Gnomad NFE exome

AF:

0.363

Gnomad OTH exome

AF:

0.368

GnomAD4 exome

AF:

0.348

AC:

414113

AN:

1189596

Hom.:

74844

Cov.:

AF XY:

0.345

AC XY:

198299

AN XY:

575466

show subpopulations

Gnomad4 AFR exome

AF:

0.320

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.361

Gnomad4 EAS exome

AF:

0.0559

Gnomad4 SAS exome

AF:

0.179

Gnomad4 FIN exome

AF:

0.414

Gnomad4 NFE exome

AF:

0.367

Gnomad4 OTH exome

AF:

0.323

GnomAD4 genome

AF:

0.332

AC:

50313

AN:

151752

Hom.:

8753

Cov.:

AF XY:

0.330

AC XY:

24467

AN XY:

74182

show subpopulations

Gnomad4 AFR

AF:

0.325

Gnomad4 AMR

AF:

0.267

Gnomad4 ASJ

AF:

0.359

Gnomad4 EAS

AF:

0.0587

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.435

Gnomad4 NFE

AF:

0.366

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.200

Hom.:

403

Bravo

AF:

0.319

TwinsUK

AF:

0.375

AC:

1391

ALSPAC

AF:

0.362

AC:

1395

ESP6500AA

AF:

0.264

AC:

630

ESP6500EA

AF:

0.298

AC:

1652

ExAC

AF:

0.218

AC:

21089

Asia WGS

AF:

0.119

AC:

410

AN:

3454

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Sep 05, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Van den Ende-Gupta syndrome

Benign:2

Jan 15, 2016

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not specified

Benign:1

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

CADD

Benign

9.6

DANN

Benign

0.91

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.19

LIST_S2

Benign

0.41

T;T

MetaRNN

Benign

0.00082

T;T

MetaSVM

Benign

-0.89

PrimateAI

Uncertain

0.73

Sift4G

Benign

0.40

T;T

Vest4

0.095

ClinPred

0.0052

GERP RS

0.076

Varity_R

0.025

gMVP

0.18

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over