rs750672289
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_000522.5(HOXA13):c.607_615delGCCGCCGCC(p.Ala203_Ala205del) variant causes a conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,376 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
HOXA13
NM_000522.5 conservative_inframe_deletion
NM_000522.5 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.41
Genes affected
HOXA13 (HGNC:5102): (homeobox A13) In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. Expansion of a polyalanine tract in the encoded protein can cause hand-foot-uterus syndrome, also known as hand-foot-genital syndrome. [provided by RefSeq, Jul 2008]
HOTTIP (HGNC:37461): (HOXA distal transcript antisense RNA) This gene produces a long RNA in antisense to the HOXA gene cluster. This transcript may regulate expression of HOXA genes in cis. This gene is upregulated in tumors and is implicated in the promotion of cell proliferation. [provided by RefSeq, Dec 2017]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_000522.5
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| HOXA13 | ENST00000649031.1 | c.607_615delGCCGCCGCC | p.Ala203_Ala205del | conservative_inframe_deletion | Exon 1 of 2 | NM_000522.5 | ENSP00000497112.1 | |||
| HOTTIP | ENST00000421733.1 | n.167+731_167+739delGGCGGCGGC | intron_variant | Intron 1 of 1 | 5 | |||||
| HOTTIP | ENST00000605136.6 | n.86+142_86+150delGGCGGCGGC | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes 0.0000132 AC: 2AN: 151906Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460470Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 726550
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GnomAD4 genome 0.0000132 AC: 2AN: 151906Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74208
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at