NM_130386.3:c.58+47276C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_130386.3(COLEC12):​c.58+47276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,916 control chromosomes in the GnomAD database, including 7,325 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.30 ( 7325 hom., cov: 31)

Consequence

COLEC12
NM_130386.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.307

Publications

3 publications found
Variant links:
Genes affected
COLEC12 (HGNC:16016): (collectin subfamily member 12) This gene encodes a member of the C-lectin family, proteins that possess collagen-like sequences and carbohydrate recognition domains. This protein is a scavenger receptor that displays several functions associated with host defense. It can bind to carbohydrate antigens on microorganisms, facilitating their recognition and removal. It also mediates the recognition, internalization, and degradation of oxidatively modified low density lipoprotein by vascular endothelial cells. [provided by RefSeq, May 2018]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COLEC12NM_130386.3 linkc.58+47276C>T intron_variant Intron 2 of 9 ENST00000400256.5 NP_569057.2 Q5KU26
COLEC12XM_011525741.3 linkc.7+67077C>T intron_variant Intron 1 of 8 XP_011524043.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COLEC12ENST00000400256.5 linkc.58+47276C>T intron_variant Intron 2 of 9 1 NM_130386.3 ENSP00000383115.3 Q5KU26
COLEC12ENST00000582147.1 linkn.266+47276C>T intron_variant Intron 2 of 8 5

Frequencies

GnomAD3 genomes
AF:
0.303
AC:
45920
AN:
151798
Hom.:
7313
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.257
Gnomad AMI
AF:
0.286
Gnomad AMR
AF:
0.425
Gnomad ASJ
AF:
0.314
Gnomad EAS
AF:
0.484
Gnomad SAS
AF:
0.305
Gnomad FIN
AF:
0.233
Gnomad MID
AF:
0.310
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.316
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.302
AC:
45951
AN:
151916
Hom.:
7325
Cov.:
31
AF XY:
0.302
AC XY:
22391
AN XY:
74256
show subpopulations
African (AFR)
AF:
0.257
AC:
10632
AN:
41402
American (AMR)
AF:
0.426
AC:
6498
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.314
AC:
1090
AN:
3472
East Asian (EAS)
AF:
0.484
AC:
2494
AN:
5148
South Asian (SAS)
AF:
0.304
AC:
1463
AN:
4806
European-Finnish (FIN)
AF:
0.233
AC:
2462
AN:
10560
Middle Eastern (MID)
AF:
0.306
AC:
90
AN:
294
European-Non Finnish (NFE)
AF:
0.299
AC:
20292
AN:
67954
Other (OTH)
AF:
0.318
AC:
669
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1576
3153
4729
6306
7882
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
454
908
1362
1816
2270
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.306
Hom.:
13082
Bravo
AF:
0.318
Asia WGS
AF:
0.396
AC:
1377
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
6.1
DANN
Benign
0.71
PhyloP100
0.31
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

Publications

Other links and lift over

dbSNP: rs2186830; hg19: chr18-433431; API