rs17801742

Variant names:

• chr12-47983086-T-C
• rs17801742
• NM_001844.5:c.2094+7A>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001844.5(COL2A1):​c.2094+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 1,613,540 control chromosomes in the GnomAD database, including 3,471 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.050 (232 hom., cov: 33)
  • Exomes 𝑓: 0.062 (3239 hom.)
• Consequence: COL2A1 NM_001844.5 splice_region, intron
• Scores: Splicing: ADA: 0.00008144
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:10
• Conservation: PhyloP100: -0.570

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]

LOC105369752 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant 12-47983086-T-C is Benign according to our data. Variant chr12-47983086-T-C is described in ClinVar as [Benign]. Clinvar id is 258223.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-47983086-T-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL2A1	NM_001844.5	c.2094+7A>G		splice_region_variant, intron_variant	Intron 32 of 53	ENST00000380518.8	NP_001835.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL2A1	ENST00000380518.8	c.2094+7A>G		splice_region_variant, intron_variant	Intron 32 of 53	1	NM_001844.5	ENSP00000369889.3
COL2A1	ENST00000337299.7	c.1887+7A>G		splice_region_variant, intron_variant	Intron 31 of 52	1		ENSP00000338213.6
COL2A1	ENST00000483376.1	n.272+7A>G		splice_region_variant, intron_variant	Intron 3 of 7	5
COL2A1	ENST00000493991.5	n.1018+7A>G		splice_region_variant, intron_variant	Intron 15 of 36	2

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7558 AN: 152012 Hom.: 233 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0293

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0119

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.0459

GnomAD3 exomes AF: 0.0454 AC: 11332 AN: 249550 Hom.: 361 AF XY: 0.0450 AC XY: 6081 AN XY: 135036

Gnomad AFR exome AF: 0.0274

Gnomad AMR exome AF: 0.0201

Gnomad ASJ exome AF: 0.0168

Gnomad EAS exome AF: 0.000272

Gnomad SAS exome AF: 0.0109

Gnomad FIN exome AF: 0.0753

Gnomad NFE exome AF: 0.0693

Gnomad OTH exome AF: 0.0469

GnomAD4 exome AF: 0.0622 AC: 90930 AN: 1461410 Hom.: 3239 Cov.: 34 AF XY: 0.0607 AC XY: 44125 AN XY: 727014

Gnomad4 AFR exome AF: 0.0263

Gnomad4 AMR exome AF: 0.0218

Gnomad4 ASJ exome AF: 0.0172

Gnomad4 EAS exome AF: 0.000428

Gnomad4 SAS exome AF: 0.0108

Gnomad4 FIN exome AF: 0.0760

Gnomad4 NFE exome AF: 0.0722

Gnomad4 OTH exome AF: 0.0535

GnomAD4 genome AF: 0.0497 AC: 7559 AN: 152130 Hom.: 232 Cov.: 33 AF XY: 0.0492 AC XY: 3659 AN XY: 74350

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.0292

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0121

Gnomad4 FIN AF: 0.0772

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0577 Hom.: 387

Bravo AF: 0.0441

Asia WGS AF: 0.0140 AC: 48 AN: 3478

EpiCase AF: 0.0564

EpiControl AF: 0.0614

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:5

Apr 08, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This 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. -

-

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:3

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 09, 2023

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Stickler syndrome type 1 Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This 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

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This 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	-0.71
CADD	Benign	8.0
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000081
dbscSNV1_RF	Benign	0.0
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

Other links and lift over

dbSNP: rs17801742; hg19: chr12-48376869;