Variant rs10204508 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.3824-31C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,608,478 control chromosomes in the GnomAD database, including 38,248 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4438 hom., cov: 33)

Exomes 𝑓: 0.21 ( 33810 hom. )

Consequence

COL3A1
NM_000090.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.131

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=-0.82).

BP6

Variant 2-189010147-C-A is Benign according to our data. Variant chr2-189010147-C-A is described in ClinVar as [Benign]. Clinvar id is 254970.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 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.3824-31C>A		intron_variant		ENST00000304636.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
COL3A1	ENST00000304636.9 linkuse as main transcript	c.3824-31C>A	intron_variant	1	NM_000090.4	P1	P02461-1
COL3A1	ENST00000450867.2 linkuse as main transcript	c.3725-31C>A	intron_variant	1
COL3A1	ENST00000487010.1 linkuse as main transcript	n.921-31C>A	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35413

AN:

151998

Hom.:

4430

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.186

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.0752

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.344

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.251

GnomAD3 exomes

AF:

0.197

AC:

49299

AN:

250534

Hom.:

5354

AF XY:

0.202

AC XY:

27346

AN XY:

135488

show subpopulations

Gnomad AFR exome

AF:

0.310

Gnomad AMR exome

AF:

0.116

Gnomad ASJ exome

AF:

0.309

Gnomad EAS exome

AF:

0.0672

Gnomad SAS exome

AF:

0.214

Gnomad FIN exome

AF:

0.150

Gnomad NFE exome

AF:

0.219

Gnomad OTH exome

AF:

0.224

GnomAD4 exome

AF:

0.211

AC:

307432

AN:

1456362

Hom.:

33810

Cov.:

AF XY:

0.212

AC XY:

153960

AN XY:

724820

show subpopulations

Gnomad4 AFR exome

AF:

0.317

Gnomad4 AMR exome

AF:

0.123

Gnomad4 ASJ exome

AF:

0.305

Gnomad4 EAS exome

AF:

0.0852

Gnomad4 SAS exome

AF:

0.217

Gnomad4 FIN exome

AF:

0.153

Gnomad4 NFE exome

AF:

0.215

Gnomad4 OTH exome

AF:

0.221

GnomAD4 genome

AF:

0.233

AC:

35436

AN:

152116

Hom.:

4438

Cov.:

AF XY:

0.230

AC XY:

17072

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.309

Gnomad4 AMR

AF:

0.186

Gnomad4 ASJ

AF:

0.294

Gnomad4 EAS

AF:

0.0750

Gnomad4 SAS

AF:

0.210

Gnomad4 FIN

AF:

0.148

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.229

Hom.:

3943

Bravo

AF:

0.239

Asia WGS

AF:

0.174

AC:

604

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Polymicrogyria with or without vascular-type Ehlers-Danlos syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Ehlers-Danlos syndrome, type 4

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.4

DANN

Benign

0.60

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