Variant rs10556764 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001378373.1(MBL2):c.-9-388_-9-383delAAAGAG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.29 ( 7808 hom., cov: 17)

Consequence

MBL2
NM_001378373.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.430

Variant links:

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]

MBL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MBL2	NM_001378373.1 linkuse as main transcript	c.-9-388_-9-383delAAAGAG		intron_variant		ENST00000674931.1	NP_001365302.1
MBL2	NM_001378374.1 linkuse as main transcript	c.-24-373_-24-368delAAAGAG		intron_variant			NP_001365303.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MBL2	ENST00000674931.1 linkuse as main transcript	c.-9-388_-9-383delAAAGAG		intron_variant			NM_001378373.1	ENSP00000502789.1		P11226
MBL2	ENST00000675947.1 linkuse as main transcript	c.-24-373_-24-368delAAAGAG		intron_variant				ENSP00000502615.1		P11226

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44278

AN:

151824

Hom.:

7795

Cov.:

show subpopulations

Gnomad AFR

AF:

0.506

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.269

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.292

AC:

44324

AN:

151942

Hom.:

7808

Cov.:

AF XY:

0.287

AC XY:

21316

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.506

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.262

Gnomad4 EAS

AF:

0.134

Gnomad4 SAS

AF:

0.245

Gnomad4 FIN

AF:

0.175

Gnomad4 NFE

AF:

0.217

Gnomad4 OTH

AF:

0.266

Alfa

AF:

0.254

Hom.:

690

Bravo

AF:

0.303

Asia WGS

AF:

0.186

AC:

648

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over