Variant rs10194475 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000090.4(COL3A1):c.3202-40G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 1,604,162 control chromosomes in the GnomAD database, including 2,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.086 ( 1191 hom., cov: 31)

Exomes 𝑓: 0.031 ( 1498 hom. )

Consequence

COL3A1
NM_000090.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.25

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 2-189006897-G-A is Benign according to our data. Variant chr2-189006897-G-A is described in ClinVar as [Benign]. Clinvar id is 254968.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL3A1	NM_000090.4 link	c.3202-40G>A		intron_variant		ENST00000304636.9	NP_000081.2	P02461-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL3A1	ENST00000304636.9 link	c.3202-40G>A		intron_variant		1	NM_000090.4	ENSP00000304408.4		P02461-1
COL3A1	ENST00000450867.2 link	c.3103-40G>A		intron_variant		1		ENSP00000415346.2		H7C435

Frequencies

GnomAD3 genomes

AF:

0.0854

AC:

12952

AN:

151714

Hom.:

1187

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0439

Gnomad ASJ

AF:

0.0262

Gnomad EAS

AF:

0.00698

Gnomad SAS

AF:

0.0164

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0286

Gnomad OTH

AF:

0.0680

GnomAD3 exomes

AF:

0.0386

AC:

9699

AN:

250988

Hom.:

511

AF XY:

0.0346

AC XY:

4694

AN XY:

135688

show subpopulations

Gnomad AFR exome

AF:

0.241

Gnomad AMR exome

AF:

0.0282

Gnomad ASJ exome

AF:

0.0196

Gnomad EAS exome

AF:

0.00724

Gnomad SAS exome

AF:

0.0153

Gnomad FIN exome

AF:

0.0206

Gnomad NFE exome

AF:

0.0295

Gnomad OTH exome

AF:

0.0380

GnomAD4 exome

AF:

0.0305

AC:

44307

AN:

1452330

Hom.:

1498

Cov.:

AF XY:

0.0295

AC XY:

21310

AN XY:

723022

show subpopulations

Gnomad4 AFR exome

AF:

0.241

Gnomad4 AMR exome

AF:

0.0296

Gnomad4 ASJ exome

AF:

0.0200

Gnomad4 EAS exome

AF:

0.00607

Gnomad4 SAS exome

AF:

0.0145

Gnomad4 FIN exome

AF:

0.0214

Gnomad4 NFE exome

AF:

0.0265

Gnomad4 OTH exome

AF:

0.0387

GnomAD4 genome

AF:

0.0855

AC:

12983

AN:

151832

Hom.:

1191

Cov.:

AF XY:

0.0832

AC XY:

6173

AN XY:

74194

show subpopulations

Gnomad4 AFR

AF:

0.237

Gnomad4 AMR

AF:

0.0438

Gnomad4 ASJ

AF:

0.0262

Gnomad4 EAS

AF:

0.00699

Gnomad4 SAS

AF:

0.0162

Gnomad4 FIN

AF:

0.0185

Gnomad4 NFE

AF:

0.0286

Gnomad4 OTH

AF:

0.0673

Alfa

AF:

0.0497

Hom.:

120

Bravo

AF:

0.0934

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 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. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.4

DANN

Benign

0.61

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