11-72003944-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_006185.4(NUMA1):c.6279C>T(p.Thr2093Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000795 in 1,613,646 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_006185.4 synonymous
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: 0.00434 AC: 661AN: 152252Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00113 AC: 282AN: 250286Hom.: 0 AF XY: 0.000812 AC XY: 110AN XY: 135488
GnomAD4 exome AF: 0.000425 AC: 621AN: 1461276Hom.: 1 Cov.: 33 AF XY: 0.000370 AC XY: 269AN XY: 726960
GnomAD4 genome AF: 0.00434 AC: 662AN: 152370Hom.: 2 Cov.: 33 AF XY: 0.00400 AC XY: 298AN XY: 74520
ClinVar
Submissions by phenotype
NUMA1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at