chr12-5494621-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001102654.2(NTF3):c.446G>A(p.Arg149Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000041 in 1,461,870 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. R149G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001102654.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NTF3 | NM_001102654.2 | c.446G>A | p.Arg149Gln | missense_variant | 2/2 | ENST00000423158.4 | |
NTF3 | NM_002527.5 | c.407G>A | p.Arg136Gln | missense_variant | 1/1 | ||
NTF3 | XM_011520963.3 | c.407G>A | p.Arg136Gln | missense_variant | 2/2 | ||
NTF3 | XM_047428901.1 | c.407G>A | p.Arg136Gln | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NTF3 | ENST00000423158.4 | c.446G>A | p.Arg149Gln | missense_variant | 2/2 | 1 | NM_001102654.2 | P4 | |
NTF3 | ENST00000331010.7 | c.407G>A | p.Arg136Gln | missense_variant | 1/1 | A1 | |||
NTF3 | ENST00000535299.5 | n.232-11944G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251372Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135880
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461870Hom.: 0 Cov.: 36 AF XY: 0.00000275 AC XY: 2AN XY: 727232
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.407G>A (p.R136Q) alteration is located in exon 1 (coding exon 1) of the NTF3 gene. This alteration results from a G to A substitution at nucleotide position 407, causing the arginine (R) at amino acid position 136 to be replaced by a glutamine (Q). 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