chr12-95682737-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021229.4(NTN4):c.1480G>A(p.Ala494Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. A494V) has been classified as Uncertain significance.
Frequency
Consequence
NM_021229.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTN4 | NM_021229.4 | c.1480G>A | p.Ala494Thr | missense_variant | 7/10 | ENST00000343702.9 | |
NTN4 | NM_001329700.2 | c.1480G>A | p.Ala494Thr | missense_variant | 7/9 | ||
NTN4 | NM_001329701.2 | c.1369G>A | p.Ala457Thr | missense_variant | 7/10 | ||
NTN4 | NM_001329702.2 | c.1369G>A | p.Ala457Thr | missense_variant | 7/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTN4 | ENST00000343702.9 | c.1480G>A | p.Ala494Thr | missense_variant | 7/10 | 1 | NM_021229.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251396Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135864
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461408Hom.: 0 Cov.: 29 AF XY: 0.00000275 AC XY: 2AN XY: 727022
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.1480G>A (p.A494T) alteration is located in exon 7 (coding exon 7) of the NTN4 gene. This alteration results from a G to A substitution at nucleotide position 1480, causing the alanine (A) at amino acid position 494 to be replaced by a threonine (T). 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