rs200333878
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_000093.5(COL5A1):c.3906+7G>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 0.000049 in 1,550,670 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000093.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.3906+7G>A | splice_region_variant, intron_variant | Intron 49 of 65 | ENST00000371817.8 | NP_000084.3 | ||
COL5A1 | NM_001278074.1 | c.3906+7G>A | splice_region_variant, intron_variant | Intron 49 of 65 | NP_001265003.1 | |||
COL5A1 | XM_017014266.3 | c.3906+7G>A | splice_region_variant, intron_variant | Intron 49 of 64 | XP_016869755.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.3906+7G>A | splice_region_variant, intron_variant | Intron 49 of 65 | 1 | NM_000093.5 | ENSP00000360882.3 | |||
COL5A1 | ENST00000371820.4 | c.3906+7G>A | splice_region_variant, intron_variant | Intron 49 of 65 | 2 | ENSP00000360885.4 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152224Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000259 AC: 4AN: 154546Hom.: 0 AF XY: 0.0000244 AC XY: 2AN XY: 81818
GnomAD4 exome AF: 0.0000508 AC: 71AN: 1398328Hom.: 0 Cov.: 32 AF XY: 0.0000391 AC XY: 27AN XY: 689726
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152342Hom.: 0 Cov.: 34 AF XY: 0.0000537 AC XY: 4AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
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not provided Benign:1
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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