chr1-9972096-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 4P and 6B. PM1PM2BP4_StrongBP6_Moderate
The NM_022787.4(NMNAT1):c.23A>C(p.Glu8Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000186 in 1,609,088 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E8K) has been classified as Uncertain significance.
Frequency
Consequence
NM_022787.4 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 |
---|---|---|---|---|---|---|---|
NMNAT1 | NM_022787.4 | c.23A>C | p.Glu8Ala | missense_variant | 2/5 | ENST00000377205.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMNAT1 | ENST00000377205.6 | c.23A>C | p.Glu8Ala | missense_variant | 2/5 | 1 | NM_022787.4 | P1 | |
NMNAT1 | ENST00000403197.5 | c.23A>C | p.Glu8Ala | missense_variant | 2/5 | 2 | |||
NMNAT1 | ENST00000492735.1 | n.107A>C | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
NMNAT1 | ENST00000462686.1 | c.23A>C | p.Glu8Ala | missense_variant, NMD_transcript_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000927 AC: 141AN: 152166Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000255 AC: 64AN: 250920Hom.: 1 AF XY: 0.000229 AC XY: 31AN XY: 135598
GnomAD4 exome AF: 0.000108 AC: 158AN: 1456802Hom.: 0 Cov.: 28 AF XY: 0.0000910 AC XY: 66AN XY: 725012
GnomAD4 genome ? AF: 0.000926 AC: 141AN: 152286Hom.: 1 Cov.: 31 AF XY: 0.000927 AC XY: 69AN XY: 74466
ClinVar
Submissions by phenotype
Leber congenital amaurosis 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at