chr2-176092982-T-TGGC
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP3BS1_Supporting
The NM_000523.4(HOXD13):c.106_108dupGCG(p.Ala36dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000469 in 1,349,830 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000523.4 conservative_inframe_insertion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000232 AC: 35AN: 150896Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000138 AC: 6AN: 43376Hom.: 0 AF XY: 0.000187 AC XY: 5AN XY: 26720
GnomAD4 exome AF: 0.000499 AC: 598AN: 1198826Hom.: 0 Cov.: 30 AF XY: 0.000489 AC XY: 287AN XY: 586546
GnomAD4 genome AF: 0.000232 AC: 35AN: 151004Hom.: 0 Cov.: 33 AF XY: 0.000230 AC XY: 17AN XY: 73768
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.106_108dup, results in the insertion of 1 amino acid(s) of the HOXD13 protein (p.Ala36dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.03%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with HOXD13-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at