Variant rs17256786 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.8305-20G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0648 in 1,614,112 control chromosomes in the GnomAD database, including 3,697 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.051 ( 268 hom., cov: 32)

Exomes 𝑓: 0.066 ( 3429 hom. )

Consequence

COL7A1
NM_000094.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.664

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=-0.79).

BP6

Variant 3-48566583-C-G is Benign according to our data. Variant chr3-48566583-C-G is described in ClinVar as [Benign]. Clinvar id is 255114.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-48566583-C-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0719 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.8305-20G>C		intron_variant		ENST00000681320.1	NP_000085.1	Q02388-1Q59F16

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
COL7A1	ENST00000681320.1 linkuse as main transcript	c.8305-20G>C	intron_variant		NM_000094.4	ENSP00000506558.1	Q02388-1
COL7A1	ENST00000328333.12 linkuse as main transcript	c.8305-20G>C	intron_variant	1		ENSP00000332371.8	Q02388-1
COL7A1	ENST00000474432.1 linkuse as main transcript	n.705-20G>C	intron_variant	3
COL7A1	ENST00000487017.5 linkuse as main transcript	n.4944-20G>C	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0509

AC:

7738

AN:

152150

Hom.:

268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0138

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.0453

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0220

Gnomad FIN

AF:

0.0877

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0736

Gnomad OTH

AF:

0.0459

GnomAD3 exomes

AF:

0.0539

AC:

13542

AN:

251462

Hom.:

463

AF XY:

0.0540

AC XY:

7336

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0126

Gnomad AMR exome

AF:

0.0318

Gnomad ASJ exome

AF:

0.0722

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0173

Gnomad FIN exome

AF:

0.0898

Gnomad NFE exome

AF:

0.0763

Gnomad OTH exome

AF:

0.0586

GnomAD4 exome

AF:

0.0662

AC:

96820

AN:

1461844

Hom.:

3429

Cov.:

AF XY:

0.0650

AC XY:

47252

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.0102

Gnomad4 AMR exome

AF:

0.0334

Gnomad4 ASJ exome

AF:

0.0712

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0192

Gnomad4 FIN exome

AF:

0.0882

Gnomad4 NFE exome

AF:

0.0747

Gnomad4 OTH exome

AF:

0.0579

GnomAD4 genome

AF:

0.0508

AC:

7734

AN:

152268

Hom.:

268

Cov.:

AF XY:

0.0508

AC XY:

3784

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0138

Gnomad4 AMR

AF:

0.0453

Gnomad4 ASJ

AF:

0.0706

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0218

Gnomad4 FIN

AF:

0.0877

Gnomad4 NFE

AF:

0.0736

Gnomad4 OTH

AF:

0.0449

Alfa

AF:

0.0629

Hom.:

Bravo

AF:

0.0469

Asia WGS

AF:

0.00924

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

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

-0.79

CADD

Benign

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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