rs644435

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_130386.3(COLEC12):​c.181+1456T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,094 control chromosomes in the GnomAD database, including 14,059 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 0.40 ( 14059 hom., cov: 32)

Consequence

COLEC12
NM_130386.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.966
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COLEC12NM_130386.3 linkuse as main transcriptc.181+1456T>C intron_variant ENST00000400256.5
COLEC12XM_011525741.3 linkuse as main transcriptc.130+1456T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COLEC12ENST00000400256.5 linkuse as main transcriptc.181+1456T>C intron_variant 1 NM_130386.3 P1
COLEC12ENST00000582147.1 linkuse as main transcriptn.389+1456T>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.401
AC:
60918
AN:
151976
Hom.:
14017
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.634
Gnomad AMI
AF:
0.195
Gnomad AMR
AF:
0.343
Gnomad ASJ
AF:
0.252
Gnomad EAS
AF:
0.107
Gnomad SAS
AF:
0.240
Gnomad FIN
AF:
0.415
Gnomad MID
AF:
0.253
Gnomad NFE
AF:
0.316
Gnomad OTH
AF:
0.352
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.401
AC:
61013
AN:
152094
Hom.:
14059
Cov.:
32
AF XY:
0.400
AC XY:
29706
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.635
Gnomad4 AMR
AF:
0.343
Gnomad4 ASJ
AF:
0.252
Gnomad4 EAS
AF:
0.107
Gnomad4 SAS
AF:
0.239
Gnomad4 FIN
AF:
0.415
Gnomad4 NFE
AF:
0.316
Gnomad4 OTH
AF:
0.347
Alfa
AF:
0.317
Hom.:
13607
Bravo
AF:
0.405
Asia WGS
AF:
0.195
AC:
683
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.3
DANN
Benign
0.42

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

LitVar

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

Other links and lift over

dbSNP: rs644435; hg19: chr18-355944; API