rs10556764

chr10-52772026-CCTCTTT-Cchr10-52772026-CCTCTTT-CCTCTTTCTCTTT

Variant summary

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

The NM_001378373.1(MBL2):c.-9-388_-9-383del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,942 control chromosomes in the GnomAD database, including 7,808 homozygotes. 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

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

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	UniProt
MBL2	NM_001378373.1	c.-9-388_-9-383del		intron_variant		ENST00000674931.1
MBL2	NM_001378374.1	c.-24-373_-24-368del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MBL2	ENST00000674931.1	c.-9-388_-9-383del		intron_variant			NM_001378373.1	P1
MBL2	ENST00000675947.1	c.-24-373_-24-368del		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44278 AN: 151824 Hom.: 7795 Cov.: 17

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.: 17 AF XY: 0.287 AC XY: 21316 AN XY: 74268

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10556764; hg19: chr10-54531786;