chr1-24419637-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_020448.5(NIPAL3):c.90C>T(p.Tyr30Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000801 in 1,613,648 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_020448.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000525 AC: 80AN: 152240Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00155 AC: 385AN: 247890Hom.: 2 AF XY: 0.00145 AC XY: 195AN XY: 134300
GnomAD4 exome AF: 0.000830 AC: 1213AN: 1461290Hom.: 16 Cov.: 30 AF XY: 0.000803 AC XY: 584AN XY: 726932
GnomAD4 genome AF: 0.000525 AC: 80AN: 152358Hom.: 1 Cov.: 32 AF XY: 0.000631 AC XY: 47AN XY: 74512
ClinVar
Submissions by phenotype
NIPAL3-related disorder Benign:1
This variant is classified as 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