15-73116673-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_002499.4(NEO1):āc.264A>Gā(p.Lys88Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000376 in 1,614,014 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_002499.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEO1 | ENST00000261908.11 | c.264A>G | p.Lys88Lys | synonymous_variant | Exon 2 of 29 | 1 | NM_002499.4 | ENSP00000261908.6 | ||
NEO1 | ENST00000558964.5 | c.264A>G | p.Lys88Lys | synonymous_variant | Exon 2 of 28 | 1 | ENSP00000453200.1 | |||
NEO1 | ENST00000560262.5 | c.264A>G | p.Lys88Lys | synonymous_variant | Exon 2 of 28 | 1 | ENSP00000453317.1 | |||
NEO1 | ENST00000339362.9 | c.264A>G | p.Lys88Lys | synonymous_variant | Exon 3 of 30 | 5 | ENSP00000341198.5 |
Frequencies
GnomAD3 genomes AF: 0.00212 AC: 323AN: 152152Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000446 AC: 112AN: 250956Hom.: 0 AF XY: 0.000347 AC XY: 47AN XY: 135642
GnomAD4 exome AF: 0.000195 AC: 285AN: 1461744Hom.: 1 Cov.: 31 AF XY: 0.000157 AC XY: 114AN XY: 727156
GnomAD4 genome AF: 0.00211 AC: 322AN: 152270Hom.: 2 Cov.: 32 AF XY: 0.00227 AC XY: 169AN XY: 74452
ClinVar
Submissions by phenotype
NEO1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at