rs17116350
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000494.4(COL17A1):āc.4109A>Gā(p.Asp1370Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,613,936 control chromosomes in the GnomAD database, including 50,100 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. D1370D) has been classified as Likely benign.
Frequency
Consequence
NM_000494.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL17A1 | NM_000494.4 | c.4109A>G | p.Asp1370Gly | missense_variant | 52/56 | ENST00000648076.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL17A1 | ENST00000648076.2 | c.4109A>G | p.Asp1370Gly | missense_variant | 52/56 | NM_000494.4 | A2 | ||
COL17A1 | ENST00000369733.8 | c.3863A>G | p.Asp1288Gly | missense_variant | 47/51 | 5 | P4 | ||
COL17A1 | ENST00000647647.1 | c.140A>G | p.Asp47Gly | missense_variant, NMD_transcript_variant | 1/5 |
Frequencies
GnomAD3 genomes ? AF: 0.277 AC: 42141AN: 151950Hom.: 6090 Cov.: 32
GnomAD3 exomes AF: 0.244 AC: 61207AN: 251344Hom.: 7803 AF XY: 0.243 AC XY: 33002AN XY: 135870
GnomAD4 exome AF: 0.244 AC: 356318AN: 1461866Hom.: 44002 Cov.: 39 AF XY: 0.243 AC XY: 176755AN XY: 727238
GnomAD4 genome ? AF: 0.277 AC: 42171AN: 152070Hom.: 6098 Cov.: 32 AF XY: 0.275 AC XY: 20441AN XY: 74330
ClinVar
Submissions by phenotype
Junctional epidermolysis bullosa, non-Herlitz type Benign:2
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. - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at