chr3-171071247-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_015028.4(TNIK):c.3525G>A(p.Pro1175Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,603,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_015028.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 52AN: 236954Hom.: 0 AF XY: 0.000211 AC XY: 27AN XY: 128064
GnomAD4 exome AF: 0.000109 AC: 158AN: 1451648Hom.: 0 Cov.: 30 AF XY: 0.000105 AC XY: 76AN XY: 721016
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74396
ClinVar
Submissions by phenotype
TNIK-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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at