rs781656634
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000451.4(SHOX):c.864G>A(p.Glu288=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000348 in 1,498,760 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 252 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. E288E) has been classified as Likely benign.
Frequency
Consequence
NM_000451.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_000451.4 | c.864G>A | p.Glu288= | synonymous_variant | 5/5 | ENST00000686671.1 | |
SHOX | NM_006883.2 | c.633+3534G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000686671.1 | c.864G>A | p.Glu288= | synonymous_variant | 5/5 | NM_000451.4 | P1 | ||
SHOX | ENST00000381575.6 | c.633+3534G>A | intron_variant | 1 | |||||
SHOX | ENST00000381578.6 | c.864G>A | p.Glu288= | synonymous_variant | 6/6 | 5 | P1 | ||
SHOX | ENST00000334060.8 | c.633+3534G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00197 AC: 299AN: 152122Hom.: 0 Cov.: 33 AF XY: 0.00198 AC XY: 147AN XY: 74316
GnomAD3 exomes AF: 0.000164 AC: 16AN: 97800Hom.: 0 AF XY: 0.000147 AC XY: 8AN XY: 54600
GnomAD4 exome AF: 0.000165 AC: 222AN: 1346530Hom.: 0 Cov.: 32 AF XY: 0.000158 AC XY: 105AN XY: 663776
GnomAD4 genome AF: 0.00197 AC: 300AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.00197 AC XY: 147AN XY: 74434
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 06, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 09, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at