dbSNP rs691773: MRC1:c.1635-681A>G (chr10-17862853-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002438.4(MRC1):c.1635-681A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 152,164 control chromosomes in the GnomAD database, including 60,260 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 0.89 ( 60255 hom., cov: 32)

Exomes 𝑓: 0.81 ( 5 hom. )

Consequence

MRC1
NM_002438.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.693

Publications

0 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:

ENSG00000235637 (HGNC:):

ENSG00000235637 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002438.4. 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
	MRC1	NM_002438.4	MANE Select	c.1635-681A>G		intron	N/A	NP_002429.1	P22897-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MRC1	ENST00000569591.3	TSL:1 MANE Select	c.1635-681A>G	intron	N/A	ENSP00000455897.1	P22897-1
MRC1	ENST00000954013.1		c.1521-681A>G	intron	N/A	ENSP00000624072.1
MRC1	ENST00000884128.1		c.1461-681A>G	intron	N/A	ENSP00000554187.1

Frequencies

GnomAD3 genomes

AF:

0.890

AC:

135255

AN:

152030

Hom.:

60191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.861

Gnomad AMI

AF:

0.971

Gnomad AMR

AF:

0.894

Gnomad ASJ

AF:

0.944

Gnomad EAS

AF:

0.861

Gnomad SAS

AF:

0.926

Gnomad FIN

AF:

0.878

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.903

Gnomad OTH

AF:

0.889

GnomAD4 exome

AF:

0.813

AC:

AN:

Hom.:

Cov.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.786

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.890

AC:

135376

AN:

152148

Hom.:

60255

Cov.:

AF XY:

0.889

AC XY:

66130

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.862

AC:

35753

AN:

41498

American (AMR)

AF:

0.894

AC:

13674

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.944

AC:

3279

AN:

3472

East Asian (EAS)

AF:

0.862

AC:

4446

AN:

5160

South Asian (SAS)

AF:

0.927

AC:

4469

AN:

4822

European-Finnish (FIN)

AF:

0.878

AC:

9289

AN:

10578

Middle Eastern (MID)

AF:

0.874

AC:

257

AN:

294

European-Non Finnish (NFE)

AF:

0.903

AC:

61445

AN:

68010

Other (OTH)

AF:

0.889

AC:

1878

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

773

1546

2318

3091

3864

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<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:

0.897

Hom.:

5184

Bravo

AF:

0.889

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.35

(source)

DANN

Benign

0.72

PhyloP100

-0.69

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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