15-73116684-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002499.4(NEO1):āc.275T>Cā(p.Phe92Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,613,912 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 (ā ).
Frequency
Consequence
NM_002499.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEO1 | ENST00000261908.11 | c.275T>C | p.Phe92Ser | missense_variant | Exon 2 of 29 | 1 | NM_002499.4 | ENSP00000261908.6 | ||
NEO1 | ENST00000558964.5 | c.275T>C | p.Phe92Ser | missense_variant | Exon 2 of 28 | 1 | ENSP00000453200.1 | |||
NEO1 | ENST00000560262.5 | c.275T>C | p.Phe92Ser | missense_variant | Exon 2 of 28 | 1 | ENSP00000453317.1 | |||
NEO1 | ENST00000339362.9 | c.275T>C | p.Phe92Ser | missense_variant | Exon 3 of 30 | 5 | ENSP00000341198.5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461730Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727146
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.275T>C (p.F92S) alteration is located in exon 2 (coding exon 2) of the NEO1 gene. This alteration results from a T to C substitution at nucleotide position 275, causing the phenylalanine (F) at amino acid position 92 to be replaced by a serine (S). 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