Variant rs3216902 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000089.4(COL1A2):c.2350-124_2350-87del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 1,160,680 control chromosomes in the GnomAD database, including 64,998 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 5245 hom., cov: 24)

Exomes 𝑓: 0.38 ( 59753 hom. )

Consequence

COL1A2
NM_000089.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.20

Variant links:

Genes affected

COL1A2 (HGNC:2198): (collagen type I alpha 2 chain) This gene encodes the pro-alpha2 chain of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIB, recessive Ehlers-Danlos syndrome Classical type, idiopathic osteoporosis, and atypical Marfan syndrome. Symptoms associated with mutations in this gene, however, tend to be less severe than mutations in the gene for the alpha1 chain of type I collagen (COL1A1) reflecting the different role of alpha2 chains in matrix integrity. Three transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]

COL1A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 7-94421772-CCTACCTCCTACTCCTTGGTCTATTCCTGGTCACATGTA-C is Benign according to our data. Variant chr7-94421772-CCTACCTCCTACTCCTTGGTCTATTCCTGGTCACATGTA-C is described in ClinVar as [Benign]. Clinvar id is 1253038.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL1A2	NM_000089.4 linkuse as main transcript	c.2350-124_2350-87del		intron_variant		ENST00000297268.11	NP_000080.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
COL1A2	ENST00000297268.11 linkuse as main transcript	c.2350-124_2350-87del	intron_variant	1	NM_000089.4	ENSP00000297268	P1
COL1A2	ENST00000473573.5 linkuse as main transcript	n.687-124_687-87del	intron_variant, non_coding_transcript_variant	2
COL1A2	ENST00000497316.5 linkuse as main transcript	n.747-124_747-87del	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.237

AC:

35891

AN:

151702

Hom.:

5247

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0611

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.282

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.277

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.252

Gnomad NFE

AF:

0.311

Gnomad OTH

AF:

0.231

GnomAD4 exome

AF:

0.381

AC:

384410

AN:

1008860

Hom.:

59753

AF XY:

0.375

AC XY:

194608

AN XY:

519088

show subpopulations

Gnomad4 AFR exome

AF:

0.0733

Gnomad4 AMR exome

AF:

0.261

Gnomad4 ASJ exome

AF:

0.318

Gnomad4 EAS exome

AF:

0.274

Gnomad4 SAS exome

AF:

0.314

Gnomad4 FIN exome

AF:

0.376

Gnomad4 NFE exome

AF:

0.415

Gnomad4 OTH exome

AF:

0.339

GnomAD4 genome

AF:

0.236

AC:

35877

AN:

151820

Hom.:

5245

Cov.:

AF XY:

0.241

AC XY:

17853

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.0609

Gnomad4 AMR

AF:

0.255

Gnomad4 ASJ

AF:

0.282

Gnomad4 EAS

AF:

0.255

Gnomad4 SAS

AF:

0.276

Gnomad4 FIN

AF:

0.378

Gnomad4 NFE

AF:

0.311

Gnomad4 OTH

AF:

0.228

Alfa

AF:

0.256

Hom.:

604

Asia WGS

AF:

0.232

AC:

806

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over