rs1064797078
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2PP5_Very_Strong
The NM_000094.4(COL7A1):āc.1A>Gā(p.Met1?) variant causes a start lost, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,399,246 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (ā ā ).
Frequency
Consequence
NM_000094.4 start_lost, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL7A1 | NM_000094.4 | c.1A>G | p.Met1? | start_lost, splice_region_variant | 2/119 | ENST00000681320.1 | NP_000085.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL7A1 | ENST00000328333.12 | c.1A>G | p.Met1? | start_lost | 1/118 | 1 | ENSP00000332371 | P1 | ||
COL7A1 | ENST00000681320.1 | c.1A>G | p.Met1? | start_lost, splice_region_variant | 2/119 | NM_000094.4 | ENSP00000506558 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1399246Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1AN XY: 690468
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Recessive dystrophic epidermolysis bullosa Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Undiagnosed Diseases Network, NIH | Mar 07, 2018 | - - |
Pathogenic, no assertion criteria provided | clinical testing | Gansu Province Medical Genetics Center | - | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 04, 2023 | Observed with a pathogenic variant on the opposite allele (in trans) in patients with RDEB referred for genetic testing at GeneDx and in published literature (PMID: 29531004); Initiation codon variant in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 36139606, 29531004) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at