rs13390932
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000331462.6(HOXD1):c.653-125T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 1,600,720 control chromosomes in the GnomAD database, including 66,377 homozygotes. 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
Genomes: 𝑓 0.31 ( 7851 hom., cov: 32)
Exomes 𝑓: 0.28 ( 58526 hom. )
Consequence
HOXD1
ENST00000331462.6 intron
ENST00000331462.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.390
Genes affected
HOXD1 (HGNC:5132): (homeobox D1) This gene is a member of the Antp homeobox family and encodes a protein with a homeobox DNA-binding domain. This nuclear protein functions as a sequence-specific transcription factor that is involved in differentiation and limb development. Mutations in this gene have been associated with severe developmental defects on the anterior-posterior (a-p) limb axis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HOXD1 | NM_024501.3 | c.653-125T>C | intron_variant | ENST00000331462.6 | NP_078777.1 | |||
HOXD1 | XM_047444086.1 | c.785+2T>C | splice_donor_variant | XP_047300042.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOXD1 | ENST00000331462.6 | c.653-125T>C | intron_variant | 1 | NM_024501.3 | ENSP00000328598 | P1 |
Frequencies
GnomAD3 genomes AF: 0.307 AC: 46648AN: 151892Hom.: 7827 Cov.: 32
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GnomAD3 exomes AF: 0.245 AC: 54724AN: 222958Hom.: 7750 AF XY: 0.246 AC XY: 30026AN XY: 122300
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GnomAD4 exome AF: 0.276 AC: 399171AN: 1448710Hom.: 58526 Cov.: 34 AF XY: 0.272 AC XY: 196108AN XY: 719906
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GnomAD4 genome AF: 0.307 AC: 46721AN: 152010Hom.: 7851 Cov.: 32 AF XY: 0.301 AC XY: 22384AN XY: 74298
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at