12-47973271-G-A

Variant summary

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

The NM_001844.5(COL2A1):​c.*136C>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 0.0669 in 1,171,608 control chromosomes in the GnomAD database, including 3,078 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.057 ( 308 hom., cov: 32)
Exomes 𝑓: 0.068 ( 2770 hom. )

Consequence

COL2A1
NM_001844.5 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.717
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 12-47973271-G-A is Benign according to our data. Variant chr12-47973271-G-A is described in ClinVar as [Benign]. Clinvar id is 308898.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-47973271-G-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0775 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
COL2A1NM_001844.5 linkuse as main transcriptc.*136C>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.*136C>T 3_prime_UTR_variant 54/541 NM_001844.5 ENSP00000369889 P1P02458-2
COL2A1ENST00000493991.5 linkuse as main transcriptn.3686C>T non_coding_transcript_exon_variant 37/372

Frequencies

GnomAD3 genomes
AF:
0.0567
AC:
8617
AN:
152068
Hom.:
308
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0333
Gnomad AMI
AF:
0.0143
Gnomad AMR
AF:
0.0322
Gnomad ASJ
AF:
0.0225
Gnomad EAS
AF:
0.0168
Gnomad SAS
AF:
0.0195
Gnomad FIN
AF:
0.0925
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0794
Gnomad OTH
AF:
0.0464
GnomAD4 exome
AF:
0.0685
AC:
69792
AN:
1019422
Hom.:
2770
Cov.:
14
AF XY:
0.0667
AC XY:
35020
AN XY:
524824
show subpopulations
Gnomad4 AFR exome
AF:
0.0316
Gnomad4 AMR exome
AF:
0.0266
Gnomad4 ASJ exome
AF:
0.0216
Gnomad4 EAS exome
AF:
0.0208
Gnomad4 SAS exome
AF:
0.0221
Gnomad4 FIN exome
AF:
0.0908
Gnomad4 NFE exome
AF:
0.0807
Gnomad4 OTH exome
AF:
0.0582
GnomAD4 genome
AF:
0.0566
AC:
8619
AN:
152186
Hom.:
308
Cov.:
32
AF XY:
0.0565
AC XY:
4204
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.0333
Gnomad4 AMR
AF:
0.0322
Gnomad4 ASJ
AF:
0.0225
Gnomad4 EAS
AF:
0.0166
Gnomad4 SAS
AF:
0.0197
Gnomad4 FIN
AF:
0.0925
Gnomad4 NFE
AF:
0.0793
Gnomad4 OTH
AF:
0.0459
Alfa
AF:
0.0718
Hom.:
96
Bravo
AF:
0.0504
Asia WGS
AF:
0.0210
AC:
72
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxJun 14, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Stickler syndrome type 1 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 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 12, 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
9.7
DANN
Benign
0.81

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: rs41272777; hg19: chr12-48367054; COSMIC: COSV56743793; COSMIC: COSV56743793; API