15-77458433-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001304504.2(HMG20A):c.26C>T(p.Thr9Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,613,254 control chromosomes in the GnomAD database, including 7 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_001304504.2 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: 0.00105 AC: 160AN: 152128Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 263AN: 251192Hom.: 3 AF XY: 0.00100 AC XY: 136AN XY: 135754
GnomAD4 exome AF: 0.00147 AC: 2148AN: 1461008Hom.: 5 Cov.: 29 AF XY: 0.00142 AC XY: 1034AN XY: 726826
GnomAD4 genome AF: 0.00105 AC: 160AN: 152246Hom.: 2 Cov.: 32 AF XY: 0.000914 AC XY: 68AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at