1-152218471-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001009931.3(HRNR):c.3158G>A(p.Arg1053Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00493 in 1,612,842 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001009931.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00376 AC: 568AN: 150976Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00302 AC: 760AN: 251414Hom.: 4 AF XY: 0.00302 AC XY: 410AN XY: 135900
GnomAD4 exome AF: 0.00506 AC: 7391AN: 1461748Hom.: 21 Cov.: 122 AF XY: 0.00485 AC XY: 3524AN XY: 727176
GnomAD4 genome AF: 0.00376 AC: 568AN: 151094Hom.: 1 Cov.: 31 AF XY: 0.00370 AC XY: 273AN XY: 73814
ClinVar
Submissions by phenotype
not provided Benign:1
HRNR: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at