chr3-158105736-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001163678.2(SHOX2):c.289C>G(p.Leu97Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 1,523,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001163678.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX2 | NM_001163678.2 | c.289C>G | p.Leu97Val | missense_variant | 1/5 | ENST00000483851.7 | |
SHOX2 | NM_003030.4 | c.289C>G | p.Leu97Val | missense_variant | 1/6 | ||
SHOX2 | NM_006884.3 | c.289C>G | p.Leu97Val | missense_variant | 1/5 | ||
SHOX2 | XM_006713727.4 | c.289C>G | p.Leu97Val | missense_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX2 | ENST00000483851.7 | c.289C>G | p.Leu97Val | missense_variant | 1/5 | 2 | NM_001163678.2 | P4 | |
SHOX2 | ENST00000389589.8 | c.289C>G | p.Leu97Val | missense_variant | 1/6 | 1 | |||
SHOX2 | ENST00000441443.6 | c.289C>G | p.Leu97Val | missense_variant | 1/5 | 5 | A1 | ||
SHOX2 | ENST00000554685.2 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 151862Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000856 AC: 1AN: 116770Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 64388
GnomAD4 exome AF: 0.0000365 AC: 50AN: 1371150Hom.: 0 Cov.: 33 AF XY: 0.0000369 AC XY: 25AN XY: 676754
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151862Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74170
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 20, 2023 | The c.289C>G (p.L97V) alteration is located in exon 1 (coding exon 1) of the SHOX2 gene. This alteration results from a C to G substitution at nucleotide position 289, causing the leucine (L) at amino acid position 97 to be replaced by a valine (V). 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