chrX-644478-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM1BP4_ModerateBS2
The NM_000451.4(SHOX):āc.721T>Cā(p.Phe241Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000328 in 1,523,430 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Synonymous variant affecting the same amino acid position (i.e. F241F) has been classified as Likely benign.
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>C | p.Phe241Leu | missense_variant | 5/5 | ENST00000686671.1 | |
SHOX | NM_006883.2 | c.633+3391T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000686671.1 | c.721T>C | p.Phe241Leu | missense_variant | 5/5 | NM_000451.4 | P1 | ||
SHOX | ENST00000381575.6 | c.633+3391T>C | intron_variant | 1 | |||||
SHOX | ENST00000381578.6 | c.721T>C | p.Phe241Leu | missense_variant | 6/6 | 5 | P1 | ||
SHOX | ENST00000334060.8 | c.633+3391T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74264
GnomAD3 exomes AF: 0.0000166 AC: 2AN: 120294Hom.: 0 AF XY: 0.0000303 AC XY: 2AN XY: 66076
GnomAD4 exome AF: 0.00000292 AC: 4AN: 1371386Hom.: 0 Cov.: 32 AF XY: 0.00000295 AC XY: 2AN XY: 676932
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74264
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 19, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at