chr4-112515318-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_024019.4(NEUROG2):c.158G>C(p.Arg53Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 1,415,614 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_024019.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEUROG2 | ENST00000313341.4 | c.158G>C | p.Arg53Pro | missense_variant | Exon 2 of 2 | 1 | NM_024019.4 | ENSP00000317333.3 | ||
NEUROG2-AS1 | ENST00000504009.1 | n.-113C>G | upstream_gene_variant | 3 | ||||||
NEUROG2-AS1 | ENST00000506057.1 | n.-67C>G | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151826Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000182 AC: 23AN: 1263788Hom.: 0 Cov.: 33 AF XY: 0.0000161 AC XY: 10AN XY: 620776
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151826Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74166
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at