16-2472119-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006181.3(NTN3):c.418C>T(p.His140Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,608,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H140N) has been classified as Uncertain significance.
Frequency
Consequence
NM_006181.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000940 AC: 23AN: 244572Hom.: 0 AF XY: 0.000105 AC XY: 14AN XY: 133266
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1455944Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 724330
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.418C>T (p.H140Y) alteration is located in exon 1 (coding exon 1) of the NTN3 gene. This alteration results from a C to T substitution at nucleotide position 418, causing the histidine (H) at amino acid position 140 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at