NM_014621.3:c.160C>T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_014621.3(HOXD4):c.160C>T(p.Arg54Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,611,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000376 AC: 9AN: 239572Hom.: 0 AF XY: 0.0000228 AC XY: 3AN XY: 131710
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1459556Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726130
GnomAD4 genome AF: 0.000184 AC: 28AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.160C>T (p.R54W) alteration is located in exon 1 (coding exon 1) of the HOXD4 gene. This alteration results from a C to T substitution at nucleotide position 160, causing the arginine (R) at amino acid position 54 to be replaced by a tryptophan (W). 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