10-17910881-T-A

Position:

• chr10-17910881-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002438.4(MRC1):​c.*416T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 181,894 control chromosomes in the GnomAD database, including 46,010 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 0.71 (39061 hom., cov: 32)
  • Exomes 𝑓: 0.68 (6949 hom.)
• Consequence: MRC1 NM_002438.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRC1	NM_002438.4	c.*416T>A		3_prime_UTR_variant	30/30	ENST00000569591.3	NP_002429.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRC1	ENST00000569591.3	c.*416T>A		3_prime_UTR_variant	30/30	1	NM_002438.4	ENSP00000455897	P1

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107888 AN: 151898 Hom.: 39011 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.691

GnomAD4 exome AF: 0.675 AC: 20169 AN: 29878 Hom.: 6949 Cov.: 0 AF XY: 0.674 AC XY: 11033 AN XY: 16376

Gnomad4 AFR exome AF: 0.838

Gnomad4 AMR exome AF: 0.600

Gnomad4 ASJ exome AF: 0.703

Gnomad4 EAS exome AF: 0.489

Gnomad4 SAS exome AF: 0.651

Gnomad4 FIN exome AF: 0.773

Gnomad4 NFE exome AF: 0.702

Gnomad4 OTH exome AF: 0.694

GnomAD4 genome AF: 0.710 AC: 107990 AN: 152016 Hom.: 39061 Cov.: 32 AF XY: 0.710 AC XY: 52745 AN XY: 74298

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.695

Alfa AF: 0.706 Hom.: 3563

Bravo AF: 0.706

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.96
DANN	Benign	0.75

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

Other links and lift over

dbSNP: rs941; hg19: chr10-18199810;