15-39584094-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_003246.4(THBS1):c.810C>T(p.Cys270Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,212 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003246.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THBS1 | NM_003246.4 | c.810C>T | p.Cys270Cys | synonymous_variant | Exon 5 of 22 | ENST00000260356.6 | NP_003237.2 | |
THBS1 | XM_047432980.1 | c.810C>T | p.Cys270Cys | synonymous_variant | Exon 5 of 22 | XP_047288936.1 | ||
THBS1 | XM_011521971.3 | c.810C>T | p.Cys270Cys | synonymous_variant | Exon 5 of 21 | XP_011520273.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251414Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135890
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461874Hom.: 1 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727236
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74490
ClinVar
Submissions by phenotype
THBS1-related disorder Benign:1
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