NM_000451.4:c.870G>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000451.4(SHOX):c.870G>A(p.Leu290Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,496,816 control chromosomes in the GnomAD database, including 46 homozygotes. There are 1,678 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000451.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHOX | NM_000451.4 | c.870G>A | p.Leu290Leu | synonymous_variant | Exon 5 of 5 | ENST00000686671.1 | NP_000442.1 | |
SHOX | NM_006883.2 | c.633+3540G>A | intron_variant | Intron 5 of 5 | NP_006874.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000686671.1 | c.870G>A | p.Leu290Leu | synonymous_variant | Exon 5 of 5 | NM_000451.4 | ENSP00000508521.1 | |||
SHOX | ENST00000381575.6 | c.633+3540G>A | intron_variant | Intron 4 of 4 | 1 | ENSP00000370987.1 | ||||
SHOX | ENST00000381578.6 | c.870G>A | p.Leu290Leu | synonymous_variant | Exon 6 of 6 | 5 | ENSP00000370990.1 | |||
SHOX | ENST00000334060.8 | c.633+3540G>A | intron_variant | Intron 5 of 5 | 5 | ENSP00000335505.3 |
Frequencies
GnomAD3 genomes AF: 0.00987 AC: 1502AN: 152128Hom.: 28 Cov.: 33 AF XY: 0.00984 AC XY: 731AN XY: 74312
GnomAD3 exomes AF: 0.00275 AC: 265AN: 96440Hom.: 1 AF XY: 0.00235 AC XY: 127AN XY: 53952
GnomAD4 exome AF: 0.00156 AC: 2093AN: 1344582Hom.: 18 Cov.: 32 AF XY: 0.00141 AC XY: 937AN XY: 662750
GnomAD4 genome AF: 0.00992 AC: 1510AN: 152234Hom.: 28 Cov.: 33 AF XY: 0.00996 AC XY: 741AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:4
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not provided Benign:2
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Connective tissue disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at