Variant rs10194304 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.3202-36C>T 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 1,605,714 control chromosomes in the GnomAD database, including 2,690 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.086 ( 1189 hom., cov: 31)

Exomes 𝑓: 0.031 ( 1501 hom. )

Consequence

COL3A1
NM_000090.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.23

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 2-189006901-C-T is Benign according to our data. Variant chr2-189006901-C-T is described in ClinVar as [Benign]. Clinvar id is 254967.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 linkuse as main transcript	c.3202-36C>T		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 linkuse as main transcript	c.3202-36C>T		intron_variant		1	NM_000090.4	ENSP00000304408.4		P02461-1
COL3A1	ENST00000450867.2 linkuse as main transcript	c.3103-36C>T		intron_variant		1		ENSP00000415346.2		H7C435

Frequencies

GnomAD3 genomes

AF:

0.0854

AC:

12951

AN:

151590

Hom.:

1185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0439

Gnomad ASJ

AF:

0.0263

Gnomad EAS

AF:

0.00700

Gnomad SAS

AF:

0.0164

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.0414

Gnomad NFE

AF:

0.0286

Gnomad OTH

AF:

0.0677

GnomAD3 exomes

AF:

0.0387

AC:

9722

AN:

251022

Hom.:

515

AF XY:

0.0346

AC XY:

4701

AN XY:

135700

show subpopulations

Gnomad AFR exome

AF:

0.242

Gnomad AMR exome

AF:

0.0281

Gnomad ASJ exome

AF:

0.0196

Gnomad EAS exome

AF:

0.00756

Gnomad SAS exome

AF:

0.0155

Gnomad FIN exome

AF:

0.0207

Gnomad NFE exome

AF:

0.0295

Gnomad OTH exome

AF:

0.0379

GnomAD4 exome

AF:

0.0305

AC:

44357

AN:

1454004

Hom.:

1501

Cov.:

AF XY:

0.0295

AC XY:

21346

AN XY:

723758

show subpopulations

Gnomad4 AFR exome

AF:

0.241

Gnomad4 AMR exome

AF:

0.0296

Gnomad4 ASJ exome

AF:

0.0200

Gnomad4 EAS exome

AF:

0.00624

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:

0.0856

AC:

12983

AN:

151710

Hom.:

1189

Cov.:

AF XY:

0.0833

AC XY:

6172

AN XY:

74110

show subpopulations

Gnomad4 AFR

AF:

0.237

Gnomad4 AMR

AF:

0.0438

Gnomad4 ASJ

AF:

0.0263

Gnomad4 EAS

AF:

0.00701

Gnomad4 SAS

AF:

0.0162

Gnomad4 FIN

AF:

0.0185

Gnomad4 NFE

AF:

0.0286

Gnomad4 OTH

AF:

0.0670

Alfa

AF:

0.0480

Hom.:

122

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

-0.81

CADD

Benign

7.3

DANN

Benign

0.62

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