chr5-135535648-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006161.3(NEUROG1):c.43G>T(p.Ala15Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000189 in 1,583,282 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A15V) has been classified as Uncertain significance.
Frequency
Consequence
NM_006161.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEUROG1 | NM_006161.3 | c.43G>T | p.Ala15Ser | missense_variant | 1/1 | ENST00000314744.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEUROG1 | ENST00000314744.6 | c.43G>T | p.Ala15Ser | missense_variant | 1/1 | NM_006161.3 | P1 | ||
ENST00000698884.1 | n.496+48879C>A | intron_variant, non_coding_transcript_variant | |||||||
SLC25A48 | ENST00000698885.1 | n.364+25892C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000107 AC: 23AN: 214728Hom.: 0 AF XY: 0.000101 AC XY: 12AN XY: 118770
GnomAD4 exome AF: 0.000198 AC: 284AN: 1431038Hom.: 0 Cov.: 31 AF XY: 0.000183 AC XY: 130AN XY: 711362
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.43G>T (p.A15S) alteration is located in exon 1 (coding exon 1) of the NEUROG1 gene. This alteration results from a G to T substitution at nucleotide position 43, causing the alanine (A) at amino acid position 15 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