chr6-31862088-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000434.4(NEU1):āc.263G>Cā(p.Gly88Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00428 in 1,613,086 control chromosomes in the GnomAD database, including 235 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G88D) has been classified as Uncertain significance.
Frequency
Consequence
NM_000434.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEU1 | NM_000434.4 | c.263G>C | p.Gly88Ala | missense_variant | 2/6 | ENST00000375631.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEU1 | ENST00000375631.5 | c.263G>C | p.Gly88Ala | missense_variant | 2/6 | 1 | NM_000434.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0221 AC: 3364AN: 152206Hom.: 115 Cov.: 32
GnomAD3 exomes AF: 0.00581 AC: 1432AN: 246458Hom.: 56 AF XY: 0.00443 AC XY: 596AN XY: 134406
GnomAD4 exome AF: 0.00242 AC: 3541AN: 1460762Hom.: 121 Cov.: 31 AF XY: 0.00210 AC XY: 1523AN XY: 726694
GnomAD4 genome AF: 0.0221 AC: 3366AN: 152324Hom.: 114 Cov.: 32 AF XY: 0.0218 AC XY: 1624AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 08, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 11, 2020 | This variant is associated with the following publications: (PMID: 25153125) - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 12, 2016 | - - |
Sialidosis type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at