2-74516012-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000621092.1(TLX2):c.289C>T(p.Arg97Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000326 in 1,522,418 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000621092.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000651 AC: 99AN: 152078Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00175 AC: 213AN: 121884Hom.: 4 AF XY: 0.00139 AC XY: 95AN XY: 68588
GnomAD4 exome AF: 0.000289 AC: 396AN: 1370232Hom.: 7 Cov.: 31 AF XY: 0.000242 AC XY: 164AN XY: 677076
GnomAD4 genome AF: 0.000664 AC: 101AN: 152186Hom.: 1 Cov.: 33 AF XY: 0.000779 AC XY: 58AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 23, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at