rs141091206
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000090.4(COL3A1):c.1617C>A(p.Pro539=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,636 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 (★). Synonymous variant affecting the same amino acid position (i.e. P539P) has been classified as Likely benign.
Frequency
Consequence
NM_000090.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL3A1 | NM_000090.4 | c.1617C>A | p.Pro539= | synonymous_variant | 23/51 | ENST00000304636.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL3A1 | ENST00000304636.9 | c.1617C>A | p.Pro539= | synonymous_variant | 23/51 | 1 | NM_000090.4 | P1 | |
COL3A1 | ENST00000450867.2 | c.1518C>A | p.Pro506= | synonymous_variant | 22/50 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251060Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135820
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461636Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727116
GnomAD4 genome ? Cov.: 30
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, type 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 25, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at