rs200595318
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000093.5(COL5A1):c.924+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00039 in 1,613,822 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000093.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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COL5A1 | NM_000093.5 | c.924+14G>A | intron_variant | Intron 6 of 65 | ENST00000371817.8 | NP_000084.3 | ||
COL5A1 | NM_001278074.1 | c.924+14G>A | intron_variant | Intron 6 of 65 | NP_001265003.1 | |||
COL5A1 | XM_017014266.3 | c.924+14G>A | intron_variant | Intron 6 of 64 | XP_016869755.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000374 AC: 57AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000361 AC: 90AN: 249336Hom.: 1 AF XY: 0.000341 AC XY: 46AN XY: 134952
GnomAD4 exome AF: 0.000392 AC: 573AN: 1461616Hom.: 1 Cov.: 34 AF XY: 0.000403 AC XY: 293AN XY: 727096
GnomAD4 genome AF: 0.000374 AC: 57AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.000498 AC XY: 37AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Ehlers-Danlos syndrome type 7A Uncertain:1
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not provided Benign:1
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Ehlers-Danlos syndrome, classic type Benign:1
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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Ehlers-Danlos syndrome, classic type, 1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at