rs73664144
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000093.5(COL5A1):c.2800-18C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,613,640 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000093.5 intron
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.2800-18C>A | intron_variant | Intron 34 of 65 | ENST00000371817.8 | NP_000084.3 | ||
COL5A1 | NM_001278074.1 | c.2800-18C>A | intron_variant | Intron 34 of 65 | NP_001265003.1 | |||
COL5A1 | XM_017014266.3 | c.2800-18C>A | intron_variant | Intron 34 of 64 | XP_016869755.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00859 AC: 1308AN: 152182Hom.: 28 Cov.: 33
GnomAD3 exomes AF: 0.00240 AC: 604AN: 251438Hom.: 10 AF XY: 0.00167 AC XY: 227AN XY: 135912
GnomAD4 exome AF: 0.000897 AC: 1311AN: 1461340Hom.: 19 Cov.: 32 AF XY: 0.000721 AC XY: 524AN XY: 727044
GnomAD4 genome AF: 0.00859 AC: 1309AN: 152300Hom.: 29 Cov.: 33 AF XY: 0.00826 AC XY: 615AN XY: 74476
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, classic type, 1 Benign:2
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Fibromuscular dysplasia, multifocal Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at