dbSNP rs2253120: MRC1:p.Thr81Thr (chr10-17823255-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.243G>A(p.Thr81Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 780,544 control chromosomes in the GnomAD database, including 40,079 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 0.32 ( 7736 hom., cov: 32)

Exomes 𝑓: 0.32 ( 32343 hom. )

Consequence

MRC1
NM_002438.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.87

Publications

7 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=-0.84).

BP7

Synonymous conserved (PhyloP=-3.87 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MRC1	NM_002438.4 link	c.243G>A	p.Thr81Thr	synonymous_variant	Exon 2 of 30	ENST00000569591.3	NP_002429.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MRC1	ENST00000569591.3 link	c.243G>A	p.Thr81Thr	synonymous_variant	Exon 2 of 30	1	NM_002438.4	ENSP00000455897.1

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48292

AN:

151866

Hom.:

7730

Cov.:

show subpopulations

Gnomad AFR

AF:

0.313

Gnomad AMI

AF:

0.254

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.321

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.319

GnomAD2 exomes

AF:

0.00

AC:

AN:

223138

AF XY:

0.00

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 FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.317

AC:

199480

AN:

628560

Hom.:

32343

Cov.:

AF XY:

0.317

AC XY:

108689

AN XY:

342430

show subpopulations

African (AFR)

AF:

0.314

AC:

5562

AN:

17686

American (AMR)

AF:

0.340

AC:

14861

AN:

43730

Ashkenazi Jewish (ASJ)

AF:

0.329

AC:

6903

AN:

20980

East Asian (EAS)

AF:

0.240

AC:

8657

AN:

36070

South Asian (SAS)

AF:

0.318

AC:

22228

AN:

69790

European-Finnish (FIN)

AF:

0.279

AC:

14811

AN:

53144

Middle Eastern (MID)

AF:

0.252

AC:

1043

AN:

4142

European-Non Finnish (NFE)

AF:

0.329

AC:

115120

AN:

349938

Other (OTH)

AF:

0.311

AC:

10295

AN:

33080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

11571

23143

34714

46286

57857

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.318

AC:

48318

AN:

151984

Hom.:

7736

Cov.:

AF XY:

0.317

AC XY:

23521

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.313

AC:

12966

AN:

41438

American (AMR)

AF:

0.325

AC:

4955

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.332

AC:

1152

AN:

3470

East Asian (EAS)

AF:

0.229

AC:

1182

AN:

5164

South Asian (SAS)

AF:

0.321

AC:

1545

AN:

4816

European-Finnish (FIN)

AF:

0.275

AC:

2903

AN:

10550

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.333

AC:

22638

AN:

67970

Other (OTH)

AF:

0.314

AC:

664

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1705

3411

5116

6822

8527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.321

Hom.:

744

Bravo

AF:

0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.0030

(source)

DANN

Benign

0.74

PhyloP100

-3.9

Mutation Taster

=100/0

polymorphism

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over