rs2099903

Variant names:

• chr10-52766097-C-A
• rs2099903
• NM_001378373.1:c.*2040G>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001378373.1(MBL2):​c.*2040G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,724 control chromosomes in the GnomAD database, including 6,641 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.28 (6641 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: MBL2 NM_001378373.1 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.321
• Publications: 11 publications found

Genes affected

MBL2 (HGNC:6922): (mannose binding lectin 2) This gene encodes the soluble mannose-binding lectin or mannose-binding protein found in serum. The protein encoded belongs to the collectin family and is an important element in the innate immune system. The protein recognizes and binds to mannose and N-acetylglucosamine on many microorganisms, including bacteria, yeast, and viruses including influenza virus, HIV and SARS-CoV. This binding activates the classical complement pathway. Deficiencies of this gene have been associated with susceptibility to autoimmune and infectious diseases. [provided by RefSeq, Jun 2020]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 10-52766097-C-A is Benign according to our data. Variant chr10-52766097-C-A is described in ClinVar as Likely_benign. ClinVar VariationId is 300114.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MBL2	NM_001378373.1	c.*2040G>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000674931.1	NP_001365302.1
MBL2	NM_000242.3	c.*2040G>T		3_prime_UTR_variant	Exon 4 of 4		NP_000233.1
MBL2	NM_001378374.1	c.*2040G>T		3_prime_UTR_variant	Exon 5 of 5		NP_001365303.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MBL2	ENST00000674931.1	c.*2040G>T		3_prime_UTR_variant	Exon 5 of 5		NM_001378373.1	ENSP00000502789.1
MBL2	ENST00000373968.3	c.*2040G>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000363079.3
MBL2	ENST00000675947.1	c.*2040G>T		3_prime_UTR_variant	Exon 5 of 5			ENSP00000502615.1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42779 AN: 151606 Hom.: 6627 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.279

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.282 AC: 42835 AN: 151724 Hom.: 6641 Cov.: 32 AF XY: 0.280 AC XY: 20768 AN XY: 74144

African (AFR) AF: 0.413 AC: 17064 AN: 41346

American (AMR) AF: 0.229 AC: 3500 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 714 AN: 3452

East Asian (EAS) AF: 0.172 AC: 886 AN: 5162

South Asian (SAS) AF: 0.202 AC: 973 AN: 4820

European-Finnish (FIN) AF: 0.249 AC: 2608 AN: 10488

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16181 AN: 67888

Other (OTH) AF: 0.278 AC: 586 AN: 2110

Alfa AF: 0.248 Hom.: 4317

Bravo AF: 0.287

Asia WGS AF: 0.205 AC: 715 AN: 3474

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mannose-binding lectin deficiency Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2099903; hg19: chr10-54525857;