2-176151982-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014621.3(HOXD4):c.349G>C(p.Asp117His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014621.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HOXD4 | NM_014621.3 | c.349G>C | p.Asp117His | missense_variant | 1/2 | ENST00000306324.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HOXD4 | ENST00000306324.4 | c.349G>C | p.Asp117His | missense_variant | 1/2 | 1 | NM_014621.3 | P1 | |
HOXD3 | ENST00000432796.2 | c.-85+14983G>C | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000830 AC: 2AN: 240936Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 132000
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460936Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726754
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.349G>C (p.D117H) alteration is located in exon 1 (coding exon 1) of the HOXD4 gene. This alteration results from a G to C substitution at nucleotide position 349, causing the aspartic acid (D) at amino acid position 117 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at