rs11191910

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000494.4(COL17A1):c.1267+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,613,846 control chromosomes in the GnomAD database, including 23,941 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1795 hom., cov: 31)

Exomes 𝑓: 0.17 ( 22146 hom. )

Consequence

COL17A1
NM_000494.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -2.09

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 10-104058133-G-A is Benign according to our data. Variant chr10-104058133-G-A is described in ClinVar as [Benign]. Clinvar id is 256265.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL17A1	NM_000494.4 link	c.1267+13C>T		intron_variant	Intron 16 of 55	ENST00000648076.2	NP_000485.3	Q9UMD9-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
COL17A1	ENST00000648076.2 link	c.1267+13C>T	intron_variant	Intron 16 of 55		NM_000494.4	ENSP00000497653.1	Q9UMD9-1
COL17A1	ENST00000369733.8 link	c.1267+13C>T	intron_variant	Intron 15 of 50	5		ENSP00000358748.3	Q9UMD9-2
COL17A1	ENST00000650263.1 link	c.1219+13C>T	intron_variant	Intron 15 of 21			ENSP00000497850.1	A0A3B3ITM2

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21447

AN:

152098

Hom.:

1784

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0603

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.199

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.179

Gnomad OTH

AF:

0.145

GnomAD3 exomes

AF:

0.162

AC:

40756

AN:

251212

Hom.:

3703

AF XY:

0.168

AC XY:

22856

AN XY:

135780

show subpopulations

Gnomad AFR exome

AF:

0.0563

Gnomad AMR exome

AF:

0.121

Gnomad ASJ exome

AF:

0.221

Gnomad EAS exome

AF:

0.103

Gnomad SAS exome

AF:

0.190

Gnomad FIN exome

AF:

0.201

Gnomad NFE exome

AF:

0.179

Gnomad OTH exome

AF:

0.168

GnomAD4 exome

AF:

0.171

AC:

250176

AN:

1461630

Hom.:

22146

Cov.:

AF XY:

0.173

AC XY:

125610

AN XY:

727106

show subpopulations

Gnomad4 AFR exome

AF:

0.0562

Gnomad4 AMR exome

AF:

0.125

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.0886

Gnomad4 SAS exome

AF:

0.190

Gnomad4 FIN exome

AF:

0.197

Gnomad4 NFE exome

AF:

0.176

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.141

AC:

21471

AN:

152216

Hom.:

1795

Cov.:

AF XY:

0.143

AC XY:

10633

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0602

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.0997

Gnomad4 SAS

AF:

0.201

Gnomad4 FIN

AF:

0.199

Gnomad4 NFE

AF:

0.179

Gnomad4 OTH

AF:

0.153

Alfa

AF:

0.166

Hom.:

2356

Bravo

AF:

0.129

Asia WGS

AF:

0.184

AC:

641

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 29, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Junctional epidermolysis bullosa, non-Herlitz type

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.28

DANN

Benign

0.42

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