15-39583687-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003246.4(THBS1):c.698C>A(p.Ser233Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000273 in 1,613,660 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 Uncertain significance (★).
Frequency
Consequence
NM_003246.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THBS1 | NM_003246.4 | c.698C>A | p.Ser233Tyr | missense_variant | Exon 4 of 22 | ENST00000260356.6 | NP_003237.2 | |
THBS1 | XM_047432980.1 | c.698C>A | p.Ser233Tyr | missense_variant | Exon 4 of 22 | XP_047288936.1 | ||
THBS1 | XM_011521971.3 | c.698C>A | p.Ser233Tyr | missense_variant | Exon 4 of 21 | XP_011520273.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251166Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135802
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461584Hom.: 0 Cov.: 33 AF XY: 0.0000358 AC XY: 26AN XY: 727084
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.698C>A (p.S233Y) alteration is located in exon 4 (coding exon 3) of the THBS1 gene. This alteration results from a C to A substitution at nucleotide position 698, causing the serine (S) at amino acid position 233 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at