rs766459219
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_000522.5(HOXA13):c.921C>T(p.Pro307Pro) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000559 in 1,609,662 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P307P) has been classified as Uncertain significance.
Frequency
Consequence
NM_000522.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOXA13 | ENST00000649031.1 | c.921C>T | p.Pro307Pro | splice_region_variant, synonymous_variant | Exon 1 of 2 | NM_000522.5 | ENSP00000497112.1 | |||
HOTTIP | ENST00000421733.1 | n.167+416G>A | intron_variant | Intron 1 of 1 | 5 | |||||
HOTTIP | ENST00000605136.6 | n.-88G>A | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247350Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134164
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1457468Hom.: 0 Cov.: 33 AF XY: 0.00000552 AC XY: 4AN XY: 725128
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at