Genetic Variant NM_024027.5:c.130+1784T>C (chr2-3606254-T-C) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024027.5(COLEC11):c.130+1784T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 1,548,874 control chromosomes in the GnomAD database, including 382,192 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 36456 hom., cov: 31)

Exomes 𝑓: 0.70 ( 345736 hom. )

Consequence

COLEC11
NM_024027.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.20

Variant links:

Genes affected

COLEC11 (HGNC:17213): (collectin subfamily member 11) This gene encodes a member of the collectin family of C-type lectins that possess collagen-like sequences and carbohydrate recognition domains. Collectins are secreted proteins that play important roles in the innate immune system by binding to carbohydrate antigens on microorganisms, facilitating their recognition and removal. The encoded protein binds to multiple sugars with a preference for fucose and mannose. Mutations in this gene are a cause of 3MC syndrome-2. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

COLEC11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 2-3606254-T-C is Benign according to our data. Variant chr2-3606254-T-C is described in ClinVar as [Benign]. Clinvar id is 402557.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-3606254-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLEC11	NM_024027.5 link	c.130+1784T>C		intron_variant	Intron 2 of 6	ENST00000349077.9	NP_076932.1	Q9BWP8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLEC11	ENST00000349077.9 link	c.130+1784T>C		intron_variant	Intron 2 of 6	1	NM_024027.5	ENSP00000339168.4		Q9BWP8-1

Frequencies

GnomAD3 genomes

AF:

0.688

AC:

104553

AN:

151894

Hom.:

36423

Cov.:

show subpopulations

Gnomad AFR

AF:

0.610

Gnomad AMI

AF:

0.557

Gnomad AMR

AF:

0.760

Gnomad ASJ

AF:

0.617

Gnomad EAS

AF:

0.847

Gnomad SAS

AF:

0.883

Gnomad FIN

AF:

0.773

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.686

Gnomad OTH

AF:

0.709

GnomAD3 exomes

AF:

0.753

AC:

110397

AN:

146552

Hom.:

42301

AF XY:

0.758

AC XY:

59903

AN XY:

79032

show subpopulations

Gnomad AFR exome

AF:

0.601

Gnomad AMR exome

AF:

0.841

Gnomad ASJ exome

AF:

0.609

Gnomad EAS exome

AF:

0.844

Gnomad SAS exome

AF:

0.884

Gnomad FIN exome

AF:

0.771

Gnomad NFE exome

AF:

0.681

Gnomad OTH exome

AF:

0.707

GnomAD4 exome

AF:

0.701

AC:

978659

AN:

1396862

Hom.:

345736

Cov.:

AF XY:

0.706

AC XY:

486736

AN XY:

689028

show subpopulations

Gnomad4 AFR exome

AF:

0.608

Gnomad4 AMR exome

AF:

0.831

Gnomad4 ASJ exome

AF:

0.608

Gnomad4 EAS exome

AF:

0.844

Gnomad4 SAS exome

AF:

0.884

Gnomad4 FIN exome

AF:

0.757

Gnomad4 NFE exome

AF:

0.680

Gnomad4 OTH exome

AF:

0.700

GnomAD4 genome

AF:

0.688

AC:

104644

AN:

152012

Hom.:

36456

Cov.:

AF XY:

0.701

AC XY:

52093

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.611

Gnomad4 AMR

AF:

0.760

Gnomad4 ASJ

AF:

0.617

Gnomad4 EAS

AF:

0.848

Gnomad4 SAS

AF:

0.882

Gnomad4 FIN

AF:

0.773

Gnomad4 NFE

AF:

0.686

Gnomad4 OTH

AF:

0.711

Alfa

AF:

0.630

Hom.:

3727

Bravo

AF:

0.680

Asia WGS

AF:

0.825

AC:

2868

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.0

DANN

Benign

0.22

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over