rs10556764

Variant names:

• chr10-52772026-CCTCTTT-C
• rs10556764
• NM_001378373.1:c.-9-388_-9-383delAAAGAG

Your query was ambiguous. Multiple possible variants found:

• chr10-52772026-CCTCTTT-C
• chr10-52772026-CCTCTTT-CCTCTTTCTCTTT

Variant summary

Our verdict is Benign. The variant received -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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 6 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378373.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MBL2	NM_001378373.1	MANE Select	c.-9-388_-9-383delAAAGAG		intron	N/A	NP_001365302.1
	MBL2	NM_001378374.1		c.-24-373_-24-368delAAAGAG		intron	N/A	NP_001365303.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MBL2	ENST00000674931.1	MANE Select	c.-9-388_-9-383delAAAGAG		intron	N/A	ENSP00000502789.1
	MBL2	ENST00000675947.1		c.-24-373_-24-368delAAAGAG		intron	N/A	ENSP00000502615.1

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

African (AFR) AF: 0.506 AC: 20943 AN: 41362

American (AMR) AF: 0.211 AC: 3220 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 906 AN: 3452

East Asian (EAS) AF: 0.134 AC: 692 AN: 5150

South Asian (SAS) AF: 0.245 AC: 1182 AN: 4822

European-Finnish (FIN) AF: 0.175 AC: 1849 AN: 10580

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14726 AN: 67986

Other (OTH) AF: 0.266 AC: 562 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10556764; hg19: chr10-54531786;