rs2239402
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000451.4(SHOX):c.277+17T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,492 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 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.
Frequency
Consequence
NM_000451.4 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_000451.4 | c.277+17T>A | intron_variant | ENST00000686671.1 | |||
SHOX | NM_006883.2 | c.277+17T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000686671.1 | c.277+17T>A | intron_variant | NM_000451.4 | P1 | ||||
SHOX | ENST00000381575.6 | c.277+17T>A | intron_variant | 1 | |||||
SHOX | ENST00000334060.8 | c.277+17T>A | intron_variant | 5 | |||||
SHOX | ENST00000381578.6 | c.277+17T>A | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152158Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74308
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248660Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135190
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460216Hom.: 0 Cov.: 58 AF XY: 0.00000138 AC XY: 1AN XY: 726394
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152276Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74436
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at