12-5494832-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001102654.2(NTF3):c.657G>A(p.Arg219Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,894 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 Likely benign (★).
Frequency
Consequence
NM_001102654.2 synonymous
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTF3 | NM_001102654.2 | c.657G>A | p.Arg219Arg | synonymous_variant | 2/2 | ENST00000423158.4 | NP_001096124.1 | |
NTF3 | NM_002527.5 | c.618G>A | p.Arg206Arg | synonymous_variant | 1/1 | NP_002518.1 | ||
NTF3 | XM_011520963.3 | c.618G>A | p.Arg206Arg | synonymous_variant | 2/2 | XP_011519265.1 | ||
NTF3 | XM_047428901.1 | c.618G>A | p.Arg206Arg | synonymous_variant | 2/2 | XP_047284857.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NTF3 | ENST00000423158.4 | c.657G>A | p.Arg219Arg | synonymous_variant | 2/2 | 1 | NM_001102654.2 | ENSP00000397297.2 | ||
NTF3 | ENST00000331010.7 | c.618G>A | p.Arg206Arg | synonymous_variant | 1/1 | 6 | ENSP00000328738.6 | |||
NTF3 | ENST00000535299.5 | n.232-11733G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461894Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | NTF3: PM2:Supporting, BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.