12-5494565-G-T
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001102654.2(NTF3):c.390G>T(p.Leu130Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,980 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L130S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001102654.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTF3 | NM_001102654.2 | c.390G>T | p.Leu130Phe | missense_variant | Exon 2 of 2 | ENST00000423158.4 | NP_001096124.1 | |
NTF3 | NM_002527.5 | c.351G>T | p.Leu117Phe | missense_variant | Exon 1 of 1 | NP_002518.1 | ||
NTF3 | XM_011520963.3 | c.351G>T | p.Leu117Phe | missense_variant | Exon 2 of 2 | XP_011519265.1 | ||
NTF3 | XM_047428901.1 | c.351G>T | p.Leu117Phe | missense_variant | Exon 2 of 2 | XP_047284857.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NTF3 | ENST00000423158.4 | c.390G>T | p.Leu130Phe | missense_variant | Exon 2 of 2 | 1 | NM_001102654.2 | ENSP00000397297.2 | ||
NTF3 | ENST00000331010.7 | c.351G>T | p.Leu117Phe | missense_variant | Exon 1 of 1 | 6 | ENSP00000328738.6 | |||
NTF3 | ENST00000535299.5 | n.232-12000G>T | intron_variant | Intron 1 of 4 | 5 | |||||
NTF3 | ENST00000543548.1 | n.*64G>T | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152120Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000358 AC: 9AN: 251370 AF XY: 0.0000221 show subpopulations
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461860Hom.: 0 Cov.: 36 AF XY: 0.00000825 AC XY: 6AN XY: 727232 show subpopulations
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74308 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.351G>T (p.L117F) alteration is located in exon 1 (coding exon 1) of the NTF3 gene. This alteration results from a G to T substitution at nucleotide position 351, causing the leucine (L) at amino acid position 117 to be replaced by a phenylalanine (F). 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