15-39582246-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003246.4(THBS1):c.121C>A(p.Arg41Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,812 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THBS1 | NM_003246.4 | c.121C>A | p.Arg41Ser | missense_variant | Exon 3 of 22 | ENST00000260356.6 | NP_003237.2 | |
THBS1 | XM_047432980.1 | c.121C>A | p.Arg41Ser | missense_variant | Exon 3 of 22 | XP_047288936.1 | ||
THBS1 | XM_011521971.3 | c.121C>A | p.Arg41Ser | missense_variant | Exon 3 of 21 | XP_011520273.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250360Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135400
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461642Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727114
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.121C>A (p.R41S) alteration is located in exon 3 (coding exon 2) of the THBS1 gene. This alteration results from a C to A substitution at nucleotide position 121, causing the arginine (R) at amino acid position 41 to be replaced by a serine (S). 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