Variant chr17-50184475-CAA-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000088.4(COL1A1):c.*1025_*1026del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 118,478 control chromosomes in the GnomAD database, including 617 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.20 ( 615 hom., cov: 26)

Exomes 𝑓: 0.11 ( 2 hom. )

Consequence

COL1A1
NM_000088.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.156

Variant links:

Genes affected

COL1A1 (HGNC:2197): (collagen type I alpha 1 chain) This gene encodes the pro-alpha1 chains 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 VIIA, Ehlers-Danlos syndrome Classical type, Caffey Disease and idiopathic osteoporosis. Reciprocal translocations between chromosomes 17 and 22, where this gene and the gene for platelet-derived growth factor beta are located, are associated with a particular type of skin tumor called dermatofibrosarcoma protuberans, resulting from unregulated expression of the growth factor. Two transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]

COL1A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-50184475-CAA-C is Benign according to our data. Variant chr17-50184475-CAA-C is described in ClinVar as [Benign]. Clinvar id is 1239296.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
COL1A1	NM_000088.4 linkuse as main transcript	c.1025_1026del	3_prime_UTR_variant	51/51	ENST00000225964.10	NP_000079.2
COL1A1	XM_005257058.5 linkuse as main transcript	c.1025_1026del	3_prime_UTR_variant	49/49		XP_005257115.2
COL1A1	XM_005257059.5 linkuse as main transcript	c.1025_1026del	3_prime_UTR_variant	38/38		XP_005257116.2
COL1A1	XM_011524341.2 linkuse as main transcript	c.1025_1026del	3_prime_UTR_variant	48/48		XP_011522643.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL1A1	ENST00000225964.10 linkuse as main transcript	c.1025_1026del		3_prime_UTR_variant	51/51	1	NM_000088.4	ENSP00000225964	P1

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

14691

AN:

72824

Hom.:

616

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.222

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.0256

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.131

Gnomad MID

AF:

0.199

Gnomad NFE

AF:

0.222

Gnomad OTH

AF:

0.194

GnomAD4 exome

AF:

0.111

AC:

5087

AN:

45654

Hom.:

AF XY:

0.113

AC XY:

2394

AN XY:

21242

show subpopulations

Gnomad4 AFR exome

AF:

0.136

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.0254

Gnomad4 SAS exome

AF:

0.0951

Gnomad4 FIN exome

AF:

0.0333

Gnomad4 NFE exome

AF:

0.130

Gnomad4 OTH exome

AF:

0.122

GnomAD4 genome

AF:

0.202

AC:

14689

AN:

72824

Hom.:

615

Cov.:

AF XY:

0.196

AC XY:

6780

AN XY:

34620

show subpopulations

Gnomad4 AFR

AF:

0.220

Gnomad4 AMR

AF:

0.158

Gnomad4 ASJ

AF:

0.184

Gnomad4 EAS

AF:

0.0258

Gnomad4 SAS

AF:

0.160

Gnomad4 FIN

AF:

0.131

Gnomad4 NFE

AF:

0.222

Gnomad4 OTH

AF:

0.192

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

May 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

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