1-107324416-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001113226.3(NTNG1):c.381C>G(p.Pro127Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00069 in 1,613,822 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001113226.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00341 AC: 518AN: 152060Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00101 AC: 252AN: 250398Hom.: 2 AF XY: 0.000695 AC XY: 94AN XY: 135278
GnomAD4 exome AF: 0.000406 AC: 593AN: 1461644Hom.: 2 Cov.: 33 AF XY: 0.000316 AC XY: 230AN XY: 727122
GnomAD4 genome AF: 0.00342 AC: 521AN: 152178Hom.: 2 Cov.: 32 AF XY: 0.00327 AC XY: 243AN XY: 74410
ClinVar
Submissions by phenotype
not provided Benign:2
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NTNG1-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