chr15-73116723-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_002499.4(NEO1):c.314C>T(p.Pro105Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000805 in 1,613,908 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002499.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEO1 | ENST00000261908.11 | c.314C>T | p.Pro105Leu | missense_variant | Exon 2 of 29 | 1 | NM_002499.4 | ENSP00000261908.6 | ||
NEO1 | ENST00000558964.5 | c.314C>T | p.Pro105Leu | missense_variant | Exon 2 of 28 | 1 | ENSP00000453200.1 | |||
NEO1 | ENST00000560262.5 | c.314C>T | p.Pro105Leu | missense_variant | Exon 2 of 28 | 1 | ENSP00000453317.1 | |||
NEO1 | ENST00000339362.9 | c.314C>T | p.Pro105Leu | missense_variant | Exon 3 of 30 | 5 | ENSP00000341198.5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152042Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000139 AC: 35AN: 251048Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135674
GnomAD4 exome AF: 0.0000855 AC: 125AN: 1461748Hom.: 1 Cov.: 32 AF XY: 0.000114 AC XY: 83AN XY: 727156
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152160Hom.: 1 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.314C>T (p.P105L) alteration is located in exon 2 (coding exon 2) of the NEO1 gene. This alteration results from a C to T substitution at nucleotide position 314, causing the proline (P) at amino acid position 105 to be replaced by a leucine (L). 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