2-176093057-G-GGGC
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP3BP6_Moderate
The NM_000523.4(HOXD13):c.180_182dup(p.Ala70dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000245 in 150,896 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00025 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00045 ( 2 hom. )
Failed GnomAD Quality Control
Consequence
HOXD13
NM_000523.4 inframe_insertion
NM_000523.4 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.191
Genes affected
HOXD13 (HGNC:5136): (homeobox D13) This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. Mutations in this particular gene cause synpolydactyly. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_000523.4
BP6
Variant 2-176093057-G-GGGC is Benign according to our data. Variant chr2-176093057-G-GGGC is described in ClinVar as [Likely_benign]. Clinvar id is 1338819.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HOXD13 | NM_000523.4 | c.180_182dup | p.Ala70dup | inframe_insertion | 1/2 | ENST00000392539.4 | NP_000514.2 | |
HOXD13 | XM_011511068.3 | c.725-1410_725-1408dup | intron_variant | XP_011509370.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOXD13 | ENST00000392539.4 | c.180_182dup | p.Ala70dup | inframe_insertion | 1/2 | 1 | NM_000523.4 | ENSP00000376322 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000245 AC: 37AN: 150788Hom.: 0 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000452 AC: 551AN: 1219006Hom.: 2 Cov.: 30 AF XY: 0.000485 AC XY: 289AN XY: 595800
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GnomAD4 genome AF: 0.000245 AC: 37AN: 150896Hom.: 0 Cov.: 33 AF XY: 0.000217 AC XY: 16AN XY: 73668
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Brachydactyly-syndactyly syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Daryl Scott Lab, Baylor College of Medicine | Jan 27, 2022 | - - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at