chrX-644478-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_ModerateBS2
The NM_000451.4(SHOX):c.721T>A(p.Phe241Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 1,523,538 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F241L) has been classified as Uncertain significance.
Frequency
Consequence
NM_000451.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_000451.4 | c.721T>A | p.Phe241Ile | missense_variant | 5/5 | ENST00000686671.1 | |
SHOX | NM_006883.2 | c.633+3391T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000686671.1 | c.721T>A | p.Phe241Ile | missense_variant | 5/5 | NM_000451.4 | P1 | ||
SHOX | ENST00000381575.6 | c.633+3391T>A | intron_variant | 1 | |||||
SHOX | ENST00000381578.6 | c.721T>A | p.Phe241Ile | missense_variant | 6/6 | 5 | P1 | ||
SHOX | ENST00000334060.8 | c.633+3391T>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74264
GnomAD3 exomes AF: 0.0000333 AC: 4AN: 120294Hom.: 0 AF XY: 0.0000454 AC XY: 3AN XY: 66076
GnomAD4 exome AF: 0.0000124 AC: 17AN: 1371386Hom.: 0 Cov.: 32 AF XY: 0.0000177 AC XY: 12AN XY: 676932
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at