rs116005007
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BS1BS2
The NM_000094.4(COL7A1):c.1907G>T(p.Gly636Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00615 in 1,614,038 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000094.4 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL7A1 | NM_000094.4 | c.1907G>T | p.Gly636Val | missense_variant, splice_region_variant | 16/119 | ENST00000681320.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL7A1 | ENST00000681320.1 | c.1907G>T | p.Gly636Val | missense_variant, splice_region_variant | 16/119 | NM_000094.4 | P1 | ||
COL7A1 | ENST00000328333.12 | c.1907G>T | p.Gly636Val | missense_variant, splice_region_variant | 15/118 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00412 AC: 627AN: 152092Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00422 AC: 1058AN: 250912Hom.: 2 AF XY: 0.00425 AC XY: 576AN XY: 135656
GnomAD4 exome AF: 0.00636 AC: 9294AN: 1461828Hom.: 40 Cov.: 33 AF XY: 0.00615 AC XY: 4473AN XY: 727224
GnomAD4 genome ? AF: 0.00413 AC: 628AN: 152210Hom.: 2 Cov.: 32 AF XY: 0.00392 AC XY: 292AN XY: 74410
ClinVar
Submissions by phenotype
not provided Uncertain:4Benign:3
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | COL7A1: BP4, BS2 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 22, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 10, 2018 | This variant is associated with the following publications: (PMID: 32707200, 26076072, 27153395) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Epidermolysis bullosa dystrophica Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Likely benign, criteria provided, single submitter | research | Biomedical Innovation Departament, CIEMAT | Jan 28, 2019 | - - |
Recessive dystrophic epidermolysis bullosa;C0268371:Dominant dystrophic epidermolysis bullosa with absence of skin;C0432321:Pretibial dystrophic epidermolysis bullosa;C0432322:Generalized dominant dystrophic epidermolysis bullosa;C1275114:Epidermolysis bullosa pruriginosa;C1843761:Nonsyndromic congenital nail disorder 8;C1851573:Transient bullous dermolysis of the newborn Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Epidermolysis bullosa dystrophica inversa, autosomal recessive Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 02, 2020 | - - |
COL7A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 27, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at