Variant 17-50184475-C-CA 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.*1026_*1027insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 120,442 control chromosomes in the GnomAD database, including 70 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.037 ( 70 hom., cov: 26)

Exomes 𝑓: 0.11 ( 0 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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-50184475-C-CA is Benign according to our data. Variant chr17-50184475-C-CA is described in ClinVar as [Benign]. Clinvar id is 1257603.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
COL1A1	NM_000088.4 linkuse as main transcript	c.1026_1027insT	3_prime_UTR_variant	51/51	ENST00000225964.10	NP_000079.2
COL1A1	XM_005257058.5 linkuse as main transcript	c.1026_1027insT	3_prime_UTR_variant	49/49		XP_005257115.2
COL1A1	XM_005257059.5 linkuse as main transcript	c.1026_1027insT	3_prime_UTR_variant	38/38		XP_005257116.2
COL1A1	XM_011524341.2 linkuse as main transcript	c.1026_1027insT	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.1026_1027insT		3_prime_UTR_variant	51/51	1	NM_000088.4	ENSP00000225964	P1

Frequencies

GnomAD3 genomes

AF:

0.0369

AC:

2694

AN:

72992

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0848

Gnomad AMI

AF:

0.00847

Gnomad AMR

AF:

0.0343

Gnomad ASJ

AF:

0.0112

Gnomad EAS

AF:

0.00631

Gnomad SAS

AF:

0.0278

Gnomad FIN

AF:

0.00678

Gnomad MID

AF:

0.0515

Gnomad NFE

AF:

0.0159

Gnomad OTH

AF:

0.0313

GnomAD4 exome

AF:

0.105

AC:

4993

AN:

47452

Hom.:

Cov.:

AF XY:

0.105

AC XY:

2305

AN XY:

21966

show subpopulations

Gnomad4 AFR exome

AF:

0.129

Gnomad4 AMR exome

AF:

0.129

Gnomad4 ASJ exome

AF:

0.117

Gnomad4 EAS exome

AF:

0.0687

Gnomad4 SAS exome

AF:

0.0920

Gnomad4 FIN exome

AF:

0.0167

Gnomad4 NFE exome

AF:

0.109

Gnomad4 OTH exome

AF:

0.119

GnomAD4 genome

AF:

0.0369

AC:

2693

AN:

72990

Hom.:

Cov.:

AF XY:

0.0366

AC XY:

1269

AN XY:

34698

show subpopulations

Gnomad4 AFR

AF:

0.0847

Gnomad4 AMR

AF:

0.0345

Gnomad4 ASJ

AF:

0.0112

Gnomad4 EAS

AF:

0.00635

Gnomad4 SAS

AF:

0.0274

Gnomad4 FIN

AF:

0.00678

Gnomad4 NFE

AF:

0.0159

Gnomad4 OTH

AF:

0.0312

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 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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