chr12-47973403-G-A

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001844.5(COL2A1):​c.*4C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00752 in 1,614,058 control chromosomes in the GnomAD database, including 213 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 91 hom., cov: 32)
Exomes 𝑓: 0.0061 ( 122 hom. )

Consequence

COL2A1
NM_001844.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 3.46
Variant links:
Genes affected
COL2A1 (HGNC:2200): (collagen type II alpha 1 chain) This gene encodes the alpha-1 chain of type II collagen, a fibrillar collagen found in cartilage and the vitreous humor of the eye. Mutations in this gene are associated with achondrogenesis, chondrodysplasia, early onset familial osteoarthritis, SED congenita, Langer-Saldino achondrogenesis, Kniest dysplasia, Stickler syndrome type I, and spondyloepimetaphyseal dysplasia Strudwick type. In addition, defects in processing chondrocalcin, a calcium binding protein that is the C-propeptide of this collagen molecule, are also associated with chondrodysplasia. There are two transcripts identified for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 12-47973403-G-A is Benign according to our data. Variant chr12-47973403-G-A is described in ClinVar as [Benign]. Clinvar id is 308902.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-47973403-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0606 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL2A1NM_001844.5 linkuse as main transcriptc.*4C>T 3_prime_UTR_variant 54/54 ENST00000380518.8 NP_001835.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL2A1ENST00000380518.8 linkuse as main transcriptc.*4C>T 3_prime_UTR_variant 54/541 NM_001844.5 ENSP00000369889 P1P02458-2
COL2A1ENST00000493991.5 linkuse as main transcriptn.3554C>T non_coding_transcript_exon_variant 37/372
COL2A1ENST00000337299.7 linkuse as main transcript downstream_gene_variant 1 ENSP00000338213 P02458-1

Frequencies

GnomAD3 genomes
AF:
0.0213
AC:
3233
AN:
152050
Hom.:
90
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0624
Gnomad AMI
AF:
0.00768
Gnomad AMR
AF:
0.0112
Gnomad ASJ
AF:
0.0300
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00249
Gnomad FIN
AF:
0.00113
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00451
Gnomad OTH
AF:
0.0163
GnomAD3 exomes
AF:
0.00967
AC:
2431
AN:
251494
Hom.:
52
AF XY:
0.00840
AC XY:
1142
AN XY:
135922
show subpopulations
Gnomad AFR exome
AF:
0.0674
Gnomad AMR exome
AF:
0.00650
Gnomad ASJ exome
AF:
0.0342
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00307
Gnomad FIN exome
AF:
0.00148
Gnomad NFE exome
AF:
0.00511
Gnomad OTH exome
AF:
0.00945
GnomAD4 exome
AF:
0.00608
AC:
8891
AN:
1461890
Hom.:
122
Cov.:
31
AF XY:
0.00580
AC XY:
4220
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0667
Gnomad4 AMR exome
AF:
0.00693
Gnomad4 ASJ exome
AF:
0.0342
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00282
Gnomad4 FIN exome
AF:
0.00165
Gnomad4 NFE exome
AF:
0.00386
Gnomad4 OTH exome
AF:
0.0105
GnomAD4 genome
AF:
0.0213
AC:
3245
AN:
152168
Hom.:
91
Cov.:
32
AF XY:
0.0212
AC XY:
1581
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.0626
Gnomad4 AMR
AF:
0.0112
Gnomad4 ASJ
AF:
0.0300
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00229
Gnomad4 FIN
AF:
0.00113
Gnomad4 NFE
AF:
0.00451
Gnomad4 OTH
AF:
0.0161
Alfa
AF:
0.0113
Hom.:
10
Bravo
AF:
0.0255
Asia WGS
AF:
0.00635
AC:
22
AN:
3478
EpiCase
AF:
0.00605
EpiControl
AF:
0.00670

ClinVar

Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsDec 06, 2018- -
Benign, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesNov 22, 2023- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 26, 2016This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Stickler syndrome type 1 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Type II Collagenopathies Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Connective tissue disorder Benign:1
Benign, criteria provided, single submitterclinical testingGenome Diagnostics Laboratory, The Hospital for Sick ChildrenNov 13, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.32
CADD
Benign
12
DANN
Benign
0.87
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs41272773; hg19: chr12-48367186; API