10-123136262-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001105574.2(HMX3):c.212C>T(p.Ala71Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000599 in 1,369,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001105574.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000316 AC: 48AN: 151760Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000222 AC: 1AN: 45086Hom.: 0 AF XY: 0.0000367 AC XY: 1AN XY: 27278
GnomAD4 exome AF: 0.0000279 AC: 34AN: 1217652Hom.: 0 Cov.: 36 AF XY: 0.0000218 AC XY: 13AN XY: 595014
GnomAD4 genome AF: 0.000316 AC: 48AN: 151868Hom.: 0 Cov.: 32 AF XY: 0.000283 AC XY: 21AN XY: 74238
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.212C>T (p.A71V) alteration is located in exon 1 (coding exon 1) of the HMX3 gene. This alteration results from a C to T substitution at nucleotide position 212, causing the alanine (A) at amino acid position 71 to be replaced by a valine (V). 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