chr1-92247981-T-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBS1BS2_Supporting
The NM_053274.3(GLMN):c.1482A>T(p.Leu494Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,193,078 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_053274.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLMN | NM_053274.3 | c.1482A>T | p.Leu494Phe | missense_variant | 17/19 | ENST00000370360.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLMN | ENST00000370360.8 | c.1482A>T | p.Leu494Phe | missense_variant | 17/19 | 1 | NM_053274.3 | P1 | |
GLMN | ENST00000495106.5 | c.*143A>T | 3_prime_UTR_variant, NMD_transcript_variant | 16/18 | 1 | ||||
GLMN | ENST00000495852.6 | c.705A>T | p.Leu235Phe | missense_variant | 9/10 | 5 | |||
GLMN | ENST00000471465.1 | n.428A>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000233 AC: 58AN: 249216Hom.: 0 AF XY: 0.000274 AC XY: 37AN XY: 134846
GnomAD4 exome AF: 0.000160 AC: 167AN: 1040764Hom.: 1 Cov.: 15 AF XY: 0.000196 AC XY: 105AN XY: 537058
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74484
ClinVar
Submissions by phenotype
Glomuvenous malformation 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