X-154477969-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006014.5(LAGE3):c.407G>A(p.Arg136His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000107 in 1,210,660 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006014.5 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: 0.0000354 AC: 4AN: 112891Hom.: 0 Cov.: 24 AF XY: 0.0000285 AC XY: 1AN XY: 35039
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183065Hom.: 0 AF XY: 0.0000443 AC XY: 3AN XY: 67661
GnomAD4 exome AF: 0.00000820 AC: 9AN: 1097769Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 5AN XY: 363135
GnomAD4 genome AF: 0.0000354 AC: 4AN: 112891Hom.: 0 Cov.: 24 AF XY: 0.0000285 AC XY: 1AN XY: 35039
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.407G>A (p.R136H) alteration is located in exon 3 (coding exon 3) of the LAGE3 gene. This alteration results from a G to A substitution at nucleotide position 407, causing the arginine (R) at amino acid position 136 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