rs371941850
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000093.5(COL5A1):c.1774-7C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,786 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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 Likely benign (★★).
Frequency
Consequence
NM_000093.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.1774-7C>A | splice_region_variant, intron_variant | ENST00000371817.8 | NP_000084.3 | |||
COL5A1 | NM_001278074.1 | c.1774-7C>A | splice_region_variant, intron_variant | NP_001265003.1 | ||||
COL5A1 | XM_017014266.3 | c.1774-7C>A | splice_region_variant, intron_variant | XP_016869755.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.1774-7C>A | splice_region_variant, intron_variant | 1 | NM_000093.5 | ENSP00000360882.3 | ||||
COL5A1 | ENST00000371820.4 | c.1774-7C>A | splice_region_variant, intron_variant | 2 | ENSP00000360885.4 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152272Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000600 AC: 15AN: 250128Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135444
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461396Hom.: 0 Cov.: 33 AF XY: 0.0000275 AC XY: 20AN XY: 726984
GnomAD4 genome AF: 0.000210 AC: 32AN: 152390Hom.: 1 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74522
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 11, 2016 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 24, 2024 | - - |
Ehlers-Danlos syndrome, classic type, 1 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Mar 15, 2022 | - - |
Fibromuscular dysplasia, multifocal Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Mar 15, 2022 | - - |
COL5A1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 20, 2021 | 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