15-39582249-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003246.4(THBS1):āc.124A>Gā(p.Lys42Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,744 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 (ā ).
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.124A>G | p.Lys42Glu | missense_variant | Exon 3 of 22 | ENST00000260356.6 | NP_003237.2 | |
THBS1 | XM_047432980.1 | c.124A>G | p.Lys42Glu | missense_variant | Exon 3 of 22 | XP_047288936.1 | ||
THBS1 | XM_011521971.3 | c.124A>G | p.Lys42Glu | missense_variant | Exon 3 of 21 | XP_011520273.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461744Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727164
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.124A>G (p.K42E) alteration is located in exon 3 (coding exon 2) of the THBS1 gene. This alteration results from a A to G substitution at nucleotide position 124, causing the lysine (K) at amino acid position 42 to be replaced by a glutamic acid (E). 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
Publications
No publications associated with this variant yet.