dbSNP rs2985837: MRC1:p.Gln242Gln (chr10-17833763-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002438.4(MRC1):c.726G>A(p.Gln242Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 780,816 control chromosomes in the GnomAD database, including 52,106 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 10811 hom., cov: 32)

Exomes 𝑓: 0.36 ( 41295 hom. )

Consequence

MRC1
NM_002438.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.51

Publications

4 publications found

Variant links:

Genes affected

MRC1 (HGNC:7228): (mannose receptor C-type 1) The recognition of complex carbohydrate structures on glycoproteins is an important part of several biological processes, including cell-cell recognition, serum glycoprotein turnover, and neutralization of pathogens. The protein encoded by this gene is a type I membrane receptor that mediates the endocytosis of glycoproteins by macrophages. The protein has been shown to bind high-mannose structures on the surface of potentially pathogenic viruses, bacteria, and fungi so that they can be neutralized by phagocytic engulfment.[provided by RefSeq, Sep 2015]

MRC1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP7

Synonymous conserved (PhyloP=1.51 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRC1	NM_002438.4 link	c.726G>A	p.Gln242Gln	synonymous_variant	Exon 4 of 30	ENST00000569591.3	NP_002429.1	P22897-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRC1	ENST00000569591.3 link	c.726G>A	p.Gln242Gln	synonymous_variant	Exon 4 of 30	1	NM_002438.4	ENSP00000455897.1		P22897-1

Frequencies

GnomAD3 genomes

AF:

0.374

AC:

56837

AN:

151920

Hom.:

10804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.382

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.381

Gnomad OTH

AF:

0.386

GnomAD2 exomes

AF:

0.00373

AC:

785

AN:

210484

AF XY:

0.00354

show subpopulations

Gnomad AFR exome

AF:

0.00411

Gnomad AMR exome

AF:

0.00712

Gnomad ASJ exome

AF:

0.00453

Gnomad EAS exome

AF:

0.00581

Gnomad FIN exome

AF:

0.000156

Gnomad NFE exome

AF:

0.00350

Gnomad OTH exome

AF:

0.00373

GnomAD4 exome

AF:

0.358

AC:

225364

AN:

628778

Hom.:

41295

Cov.:

AF XY:

0.354

AC XY:

121350

AN XY:

342530

show subpopulations

African (AFR)

AF:

0.401

AC:

7091

AN:

17694

American (AMR)

AF:

0.366

AC:

16002

AN:

43740

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

7953

AN:

20984

East Asian (EAS)

AF:

0.298

AC:

10760

AN:

36070

South Asian (SAS)

AF:

0.277

AC:

19353

AN:

69798

European-Finnish (FIN)

AF:

0.339

AC:

18011

AN:

53144

Middle Eastern (MID)

AF:

0.293

AC:

1215

AN:

4148

European-Non Finnish (NFE)

AF:

0.380

AC:

133100

AN:

350102

Other (OTH)

AF:

0.359

AC:

11879

AN:

33098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

10368

20735

31103

41470

51838

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

822

1644

2466

3288

4110

<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:

0.374

AC:

56882

AN:

152038

Hom.:

10811

Cov.:

AF XY:

0.372

AC XY:

27639

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.400

AC:

16597

AN:

41456

American (AMR)

AF:

0.363

AC:

5552

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

1325

AN:

3466

East Asian (EAS)

AF:

0.258

AC:

1332

AN:

5154

South Asian (SAS)

AF:

0.283

AC:

1365

AN:

4818

European-Finnish (FIN)

AF:

0.334

AC:

3531

AN:

10560

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.381

AC:

25930

AN:

67990

Other (OTH)

AF:

0.386

AC:

814

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1844

3688

5533

7377

9221

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<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:

0.378

Hom.:

1148

Bravo

AF:

0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

4.7

(source)

DANN

Benign

0.75

PhyloP100

1.5

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over