NM_182895.5:c.2444C>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -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. 11/17 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

Publications

19 publications found

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 Gene-Disease associations (from GenCC):

van den Ende-Gupta syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia

SCARF2 links:

ENSG00000305663 (HGNC:):

ENSG00000305663 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 518325.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

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

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCARF2	NM_182895.5	MANE Select	c.2444C>G	p.Ala815Gly	missense	Exon 11 of 11	NP_878315.2	Q96GP6-2
	SCARF2	NM_153334.7		c.2459C>G	p.Ala820Gly	missense	Exon 11 of 11	NP_699165.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SCARF2	ENST00000622235.5	TSL:1 MANE Select	c.2444C>G	p.Ala815Gly	missense	Exon 11 of 11	ENSP00000477564.2	Q96GP6-2
SCARF2	ENST00000623402.1	TSL:1	c.2459C>G	p.Ala820Gly	missense	Exon 11 of 11	ENSP00000485276.1	Q96GP6-1
SCARF2	ENST00000925309.1		c.2573C>G	p.Ala858Gly	missense	Exon 11 of 11	ENSP00000595368.1

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

GnomAD2 exomes

AF:

0.301

AC:

7826

AN:

25994

AF XY:

0.309

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 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

African (AFR)

AF:

0.320

AC:

7733

AN:

24162

American (AMR)

AF:

0.203

AC:

2346

AN:

11566

Ashkenazi Jewish (ASJ)

AF:

0.361

AC:

5853

AN:

16222

East Asian (EAS)

AF:

0.0559

AC:

1587

AN:

28404

South Asian (SAS)

AF:

0.179

AC:

8657

AN:

48254

European-Finnish (FIN)

AF:

0.414

AC:

11489

AN:

27732

Middle Eastern (MID)

AF:

0.330

AC:

1222

AN:

3704

European-Non Finnish (NFE)

AF:

0.367

AC:

359657

AN:

981324

Other (OTH)

AF:

0.323

AC:

15569

AN:

48228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

15706

31411

47117

62822

78528

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12342

24684

37026

49368

61710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.332

AC:

50313

AN:

151752

Hom.:

8753

Cov.:

AF XY:

0.330

AC XY:

24467

AN XY:

74182

show subpopulations

African (AFR)

AF:

0.325

AC:

13465

AN:

41406

American (AMR)

AF:

0.267

AC:

4080

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.359

AC:

1243

AN:

3462

East Asian (EAS)

AF:

0.0587

AC:

302

AN:

5146

South Asian (SAS)

AF:

0.170

AC:

819

AN:

4824

European-Finnish (FIN)

AF:

0.435

AC:

4569

AN:

10514

Middle Eastern (MID)

AF:

0.298

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.366

AC:

24787

AN:

67810

Other (OTH)

AF:

0.309

AC:

651

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

1744

3488

5233

6977

8721

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

492

984

1476

1968

2460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Van den Ende-Gupta syndrome (2)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.70

CADD

Benign

9.6

(source)

DANN

Benign

0.91

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.19

LIST_S2

Benign

0.41

MetaRNN

Benign

0.00082

MetaSVM

Benign

-0.89

PhyloP100

0.75

PrimateAI

Uncertain

0.73

Sift4G

Benign

0.40

Vest4

0.095

ClinPred

0.0052

GERP RS

0.076

Varity_R

0.025

gMVP

0.18

Mutation Taster

=95/5

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over