Variant 2-188985047-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_000090.4(COL3A1):c.282+85A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 1,435,190 control chromosomes in the GnomAD database, including 139,922 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.36 ( 11604 hom., cov: 31)

Exomes 𝑓: 0.44 ( 128318 hom. )

Consequence

COL3A1
NM_000090.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.467

Variant links:

Genes affected

COL3A1 (HGNC:2201): (collagen type III alpha 1 chain) This gene encodes the pro-alpha1 chains of type III collagen, a fibrillar collagen that is found in extensible connective tissues such as skin, lung, uterus, intestine and the vascular system, frequently in association with type I collagen. Mutations in this gene are associated with Ehlers-Danlos syndrome type IV, and with aortic and arterial aneurysms. [provided by R. Dalgleish, Feb 2008]

COL3A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 2-188985047-A-G is Benign according to our data. Variant chr2-188985047-A-G is described in ClinVar as [Benign]. Clinvar id is 673782.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL3A1	NM_000090.4 linkuse as main transcript	c.282+85A>G		intron_variant		ENST00000304636.9

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL3A1	ENST00000304636.9 linkuse as main transcript	c.282+85A>G	intron_variant		1	NM_000090.4	P1	P02461-1
COL3A1	ENST00000450867.2 linkuse as main transcript	c.282+85A>G	intron_variant		1
COL3A1	ENST00000470167.1 linkuse as main transcript	n.463A>G	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.356

AC:

54020

AN:

151682

Hom.:

11604

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.448

Gnomad ASJ

AF:

0.309

Gnomad EAS

AF:

0.607

Gnomad SAS

AF:

0.454

Gnomad FIN

AF:

0.560

Gnomad MID

AF:

0.255

Gnomad NFE

AF:

0.430

Gnomad OTH

AF:

0.325

GnomAD4 exome

AF:

0.440

AC:

564256

AN:

1283388

Hom.:

128318

Cov.:

AF XY:

0.438

AC XY:

282697

AN XY:

645422

show subpopulations

Gnomad4 AFR exome

AF:

0.0944

Gnomad4 AMR exome

AF:

0.545

Gnomad4 ASJ exome

AF:

0.317

Gnomad4 EAS exome

AF:

0.581

Gnomad4 SAS exome

AF:

0.445

Gnomad4 FIN exome

AF:

0.546

Gnomad4 NFE exome

AF:

0.440

Gnomad4 OTH exome

AF:

0.414

GnomAD4 genome

AF:

0.356

AC:

54028

AN:

151802

Hom.:

11604

Cov.:

AF XY:

0.365

AC XY:

27055

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.112

Gnomad4 AMR

AF:

0.448

Gnomad4 ASJ

AF:

0.309

Gnomad4 EAS

AF:

0.606

Gnomad4 SAS

AF:

0.454

Gnomad4 FIN

AF:

0.560

Gnomad4 NFE

AF:

0.430

Gnomad4 OTH

AF:

0.326

Alfa

AF:

0.413

Hom.:

20782

Bravo

AF:

0.338

Asia WGS

AF:

0.496

AC:

1725

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 16, 2018

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.2

DANN

Benign

0.75

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