chr3-158105682-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001163678.2(SHOX2):c.343G>A(p.Glu115Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,523,644 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_001163678.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152092Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000842 AC: 1AN: 118724Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 65928
GnomAD4 exome AF: 0.00000948 AC: 13AN: 1371552Hom.: 0 Cov.: 33 AF XY: 0.0000118 AC XY: 8AN XY: 677372
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152092Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.343G>A (p.E115K) alteration is located in exon 1 (coding exon 1) of the SHOX2 gene. This alteration results from a G to A substitution at nucleotide position 343, causing the glutamic acid (E) at amino acid position 115 to be replaced by a lysine (K). 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