1-161229790-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_005122.5(NR1I3):c.*7G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000294 in 1,614,210 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 Likely benign (no stars).
Frequency
Consequence
NM_005122.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000271 AC: 68AN: 250578Hom.: 0 AF XY: 0.000317 AC XY: 43AN XY: 135516
GnomAD4 exome AF: 0.000306 AC: 447AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.000296 AC XY: 215AN XY: 727248
GnomAD4 genome AF: 0.000177 AC: 27AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74486
ClinVar
Submissions by phenotype
TOMM40L-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