Variant chr10-104031871-CA-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_000494.4(COL17A1):c.*363del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 319,058 control chromosomes in the GnomAD database, including 7,573 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4197 hom., cov: 27)

Exomes 𝑓: 0.19 ( 3376 hom. )

Consequence

COL17A1
NM_000494.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.109

Variant links:

Genes affected

COL17A1 (HGNC:2194): (collagen type XVII alpha 1 chain) This gene encodes the alpha chain of type XVII collagen. Unlike most collagens, collagen XVII is a transmembrane protein. Collagen XVII is a structural component of hemidesmosomes, multiprotein complexes at the dermal-epidermal basement membrane zone that mediate adhesion of keratinocytes to the underlying membrane. Mutations in this gene are associated with both generalized atrophic benign and junctional epidermolysis bullosa. Two homotrimeric forms of type XVII collagen exist. The full length form is the transmembrane protein. A soluble form, referred to as either ectodomain or LAD-1, is generated by proteolytic processing of the full length form. [provided by RefSeq, Jul 2008]

COL17A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-104031871-CA-C is Benign according to our data. Variant chr10-104031871-CA-C is described in ClinVar as [Benign]. Clinvar id is 298676.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL17A1	NM_000494.4 linkuse as main transcript	c.*363del		3_prime_UTR_variant	56/56	ENST00000648076.2	NP_000485.3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL17A1	ENST00000648076.2 linkuse as main transcript	c.*363del	3_prime_UTR_variant	56/56		NM_000494.4	ENSP00000497653	A2	Q9UMD9-1
COL17A1	ENST00000369733.8 linkuse as main transcript	c.*363del	3_prime_UTR_variant	51/51	5		ENSP00000358748	P4	Q9UMD9-2
COL17A1	ENST00000433822.1 linkuse as main transcript	c.*32-279del	intron_variant		5		ENSP00000388832
COL17A1	ENST00000647647.1 linkuse as main transcript	c.*927del	3_prime_UTR_variant, NMD_transcript_variant	5/5			ENSP00000497865

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34366

AN:

151760

Hom.:

4177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.310

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.280

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.215

GnomAD4 exome

AF:

0.192

AC:

32021

AN:

167180

Hom.:

3376

Cov.:

AF XY:

0.197

AC XY:

17381

AN XY:

88272

show subpopulations

Gnomad4 AFR exome

AF:

0.297

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.167

Gnomad4 EAS exome

AF:

0.117

Gnomad4 SAS exome

AF:

0.258

Gnomad4 FIN exome

AF:

0.219

Gnomad4 NFE exome

AF:

0.178

Gnomad4 OTH exome

AF:

0.191

GnomAD4 genome

AF:

0.227

AC:

34448

AN:

151878

Hom.:

4197

Cov.:

AF XY:

0.228

AC XY:

16936

AN XY:

74210

show subpopulations

Gnomad4 AFR

AF:

0.311

Gnomad4 AMR

AF:

0.186

Gnomad4 ASJ

AF:

0.164

Gnomad4 EAS

AF:

0.127

Gnomad4 SAS

AF:

0.281

Gnomad4 FIN

AF:

0.238

Gnomad4 NFE

AF:

0.190

Gnomad4 OTH

AF:

0.221

Alfa

AF:

0.0945

Hom.:

131

Bravo

AF:

0.225

Asia WGS

AF:

0.256

AC:

892

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Junctional epidermolysis bullosa

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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