rs2289080
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005199.5(CHRNG):c.445G>A(p.Ala149Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0243 in 1,614,044 control chromosomes in the GnomAD database, including 865 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005199.5 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 |
---|---|---|---|---|---|---|---|
CHRNG | NM_005199.5 | c.445G>A | p.Ala149Thr | missense_variant | 5/12 | ENST00000651502.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNG | ENST00000651502.1 | c.445G>A | p.Ala149Thr | missense_variant | 5/12 | NM_005199.5 | P1 | ||
CHRNG | ENST00000389492.3 | c.350+757G>A | intron_variant | 1 | |||||
CHRNG | ENST00000485094.1 | n.466G>A | non_coding_transcript_exon_variant | 5/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0278 AC: 4227AN: 152134Hom.: 103 Cov.: 32
GnomAD3 exomes AF: 0.0335 AC: 8415AN: 251456Hom.: 229 AF XY: 0.0312 AC XY: 4240AN XY: 135906
GnomAD4 exome AF: 0.0239 AC: 34990AN: 1461792Hom.: 762 Cov.: 31 AF XY: 0.0239 AC XY: 17368AN XY: 727208
GnomAD4 genome ? AF: 0.0279 AC: 4244AN: 152252Hom.: 103 Cov.: 32 AF XY: 0.0285 AC XY: 2121AN XY: 74432
ClinVar
Submissions by phenotype
Autosomal recessive multiple pterygium syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 25, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Congenital Myasthenic Syndrome, Dominant/Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Lethal multiple pterygium syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 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