rs143764154
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002499.4(NEO1):c.295G>A(p.Asp99Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000403 in 1,613,838 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 (★).
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.295G>A | p.Asp99Asn | missense_variant | Exon 2 of 29 | 1 | NM_002499.4 | ENSP00000261908.6 | ||
NEO1 | ENST00000558964.5 | c.295G>A | p.Asp99Asn | missense_variant | Exon 2 of 28 | 1 | ENSP00000453200.1 | |||
NEO1 | ENST00000560262.5 | c.295G>A | p.Asp99Asn | missense_variant | Exon 2 of 28 | 1 | ENSP00000453317.1 | |||
NEO1 | ENST00000339362.9 | c.295G>A | p.Asp99Asn | missense_variant | Exon 3 of 30 | 5 | ENSP00000341198.5 |
Frequencies
GnomAD3 genomes AF: 0.000447 AC: 68AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000231 AC: 58AN: 251042Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135678
GnomAD4 exome AF: 0.000399 AC: 583AN: 1461760Hom.: 0 Cov.: 31 AF XY: 0.000407 AC XY: 296AN XY: 727170
GnomAD4 genome AF: 0.000447 AC: 68AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.000431 AC XY: 32AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.295G>A (p.D99N) alteration is located in exon 2 (coding exon 2) of the NEO1 gene. This alteration results from a G to A substitution at nucleotide position 295, causing the aspartic acid (D) at amino acid position 99 to be replaced by an asparagine (N). 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