Variant chr3-48571073-T-C 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_000094.4(COL7A1):c.7164+28A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 1,612,936 control chromosomes in the GnomAD database, including 7,668 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 3367 hom., cov: 32)

Exomes 𝑓: 0.047 ( 4301 hom. )

Consequence

COL7A1
NM_000094.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.44

Variant links:

Genes affected

COL7A1 (HGNC:2214): (collagen type VII alpha 1 chain) This gene encodes the alpha chain of type VII collagen. The type VII collagen fibril, composed of three identical alpha collagen chains, is restricted to the basement zone beneath stratified squamous epithelia. It functions as an anchoring fibril between the external epithelia and the underlying stroma. Mutations in this gene are associated with all forms of dystrophic epidermolysis bullosa. In the absence of mutations, however, an acquired form of this disease can result from an autoimmune response made to type VII collagen. [provided by RefSeq, Jul 2008]

COL7A1 links:

COL7A1 (HGNC:):

COL7A1 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=-0.91).

BP6

Variant 3-48571073-T-C is Benign according to our data. Variant chr3-48571073-T-C is described in ClinVar as [Benign]. Clinvar id is 1223033.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL7A1	NM_000094.4 linkuse as main transcript	c.7164+28A>G		intron_variant		ENST00000681320.1	NP_000085.1	Q02388-1Q59F16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL7A1	ENST00000681320.1 linkuse as main transcript	c.7164+28A>G		intron_variant			NM_000094.4	ENSP00000506558.1		Q02388-1

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21466

AN:

151938

Hom.:

3347

Cov.:

show subpopulations

Gnomad AFR

AF:

0.385

Gnomad AMI

AF:

0.0418

Gnomad AMR

AF:

0.0830

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.0484

Gnomad FIN

AF:

0.0400

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0341

Gnomad OTH

AF:

0.135

GnomAD3 exomes

AF:

0.0701

AC:

17483

AN:

249294

Hom.:

1538

AF XY:

0.0631

AC XY:

8551

AN XY:

135424

show subpopulations

Gnomad AFR exome

AF:

0.387

Gnomad AMR exome

AF:

0.0503

Gnomad ASJ exome

AF:

0.114

Gnomad EAS exome

AF:

0.108

Gnomad SAS exome

AF:

0.0468

Gnomad FIN exome

AF:

0.0388

Gnomad NFE exome

AF:

0.0349

Gnomad OTH exome

AF:

0.0675

GnomAD4 exome

AF:

0.0471

AC:

68783

AN:

1460880

Hom.:

4301

Cov.:

AF XY:

0.0461

AC XY:

33520

AN XY:

726780

show subpopulations

Gnomad4 AFR exome

AF:

0.408

Gnomad4 AMR exome

AF:

0.0544

Gnomad4 ASJ exome

AF:

0.109

Gnomad4 EAS exome

AF:

0.0916

Gnomad4 SAS exome

AF:

0.0462

Gnomad4 FIN exome

AF:

0.0399

Gnomad4 NFE exome

AF:

0.0312

Gnomad4 OTH exome

AF:

0.0773

GnomAD4 genome

AF:

0.142

AC:

21535

AN:

152056

Hom.:

3367

Cov.:

AF XY:

0.140

AC XY:

10389

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.386

Gnomad4 AMR

AF:

0.0826

Gnomad4 ASJ

AF:

0.107

Gnomad4 EAS

AF:

0.110

Gnomad4 SAS

AF:

0.0482

Gnomad4 FIN

AF:

0.0400

Gnomad4 NFE

AF:

0.0341

Gnomad4 OTH

AF:

0.137

Alfa

AF:

0.0671

Hom.:

646

Bravo

AF:

0.156

Asia WGS

AF:

0.147

AC:

512

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.57

DANN

Benign

0.30

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