NM_000090.4:c.996+10T>A
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_000090.4(COL3A1):c.996+10T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000090.4 intron
Scores
Clinical Significance
Conservation
Publications
- autosomal dominant Ehlers-Danlos syndrome, vascular typeInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Genomics England PanelApp
- Ehlers-Danlos syndrome, vascular typeInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
- polymicrogyria with or without vascular-type Ehlers-Danlos syndromeInheritance: AR Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636.9 | c.996+10T>A | intron_variant | Intron 14 of 50 | 1 | NM_000090.4 | ENSP00000304408.4 | |||
COL3A1 | ENST00000450867.2 | c.996+10T>A | intron_variant | Intron 14 of 49 | 1 | ENSP00000415346.2 | ||||
COL3A1 | ENST00000713745.1 | c.996+10T>A | intron_variant | Intron 14 of 48 | ENSP00000519049.1 | |||||
COL3A1 | ENST00000713744.1 | c.996+10T>A | intron_variant | Intron 14 of 48 | ENSP00000519048.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000199 AC: 5AN: 251398 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461136Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 726936 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74318 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
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 4 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at