rs805701

Positions:

chr10-104060198-G-A

Variant summary

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

The NM_000494.4(COL17A1):c.1062C>T(p.Ala354=) variant causes a synonymous change. The variant allele was found at a frequency of 0.661 in 1,613,894 control chromosomes in the GnomAD database, including 358,427 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 27083 hom., cov: 31)

Exomes 𝑓: 0.67 ( 331344 hom. )

Consequence

COL17A1
NM_000494.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 4.61

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=-0.49).

BP6

Variant 10-104060198-G-A is Benign according to our data. Variant chr10-104060198-G-A is described in ClinVar as [Benign]. Clinvar id is 256263.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-104060198-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL17A1	NM_000494.4 linkuse as main transcript	c.1062C>T	p.Ala354=	synonymous_variant	14/56	ENST00000648076.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL17A1	ENST00000648076.2 linkuse as main transcript	c.1062C>T	p.Ala354=	synonymous_variant	14/56		NM_000494.4	A2	Q9UMD9-1

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87244

AN:

151906

Hom.:

27082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.662

Gnomad AMR

AF:

0.678

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.694

Gnomad SAS

AF:

0.629

Gnomad FIN

AF:

0.666

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.678

Gnomad OTH

AF:

0.596

GnomAD3 exomes

AF:

0.657

AC:

165344

AN:

251492

Hom.:

55822

AF XY:

0.659

AC XY:

89546

AN XY:

135920

show subpopulations

Gnomad AFR exome

AF:

0.310

Gnomad AMR exome

AF:

0.759

Gnomad ASJ exome

AF:

0.647

Gnomad EAS exome

AF:

0.695

Gnomad SAS exome

AF:

0.634

Gnomad FIN exome

AF:

0.657

Gnomad NFE exome

AF:

0.678

Gnomad OTH exome

AF:

0.657

GnomAD4 exome

AF:

0.670

AC:

979289

AN:

1461870

Hom.:

331344

Cov.:

AF XY:

0.669

AC XY:

486699

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.300

Gnomad4 AMR exome

AF:

0.748

Gnomad4 ASJ exome

AF:

0.655

Gnomad4 EAS exome

AF:

0.709

Gnomad4 SAS exome

AF:

0.634

Gnomad4 FIN exome

AF:

0.658

Gnomad4 NFE exome

AF:

0.682

Gnomad4 OTH exome

AF:

0.645

GnomAD4 genome

AF:

0.574

AC:

87259

AN:

152024

Hom.:

27083

Cov.:

AF XY:

0.577

AC XY:

42877

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.309

Gnomad4 AMR

AF:

0.678

Gnomad4 ASJ

AF:

0.669

Gnomad4 EAS

AF:

0.694

Gnomad4 SAS

AF:

0.630

Gnomad4 FIN

AF:

0.666

Gnomad4 NFE

AF:

0.678

Gnomad4 OTH

AF:

0.590

Alfa

AF:

0.657

Hom.:

64910

Bravo

AF:

0.564

Asia WGS

AF:

0.563

AC:

1958

AN:

3478

EpiCase

AF:

0.680

EpiControl

AF:

0.675

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Junctional epidermolysis bullosa, non-Herlitz type

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	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. -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Epithelial recurrent erosion dystrophy

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

-0.49

CADD

Benign

DANN

Benign

0.59

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