chr1-92247304-CAG-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_053274.3(GLMN):c.1586-162_1586-161del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,892 control chromosomes in the GnomAD database, including 6,481 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.26 ( 6481 hom., cov: 23)
Consequence
GLMN
NM_053274.3 intron
NM_053274.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.421
Genes affected
GLMN (HGNC:14373): (glomulin, FKBP associated protein) This gene encodes a phosphorylated protein that is a member of a Skp1-Cullin-F-box-like complex. The protein is essential for normal development of the vasculature and mutations in this gene have been associated with glomuvenous malformations, also called glomangiomas. Multiple splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 1-92247304-CAG-C is Benign according to our data. Variant chr1-92247304-CAG-C is described in ClinVar as [Benign]. Clinvar id is 1294738.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLMN | NM_053274.3 | c.1586-162_1586-161del | intron_variant | ENST00000370360.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLMN | ENST00000370360.8 | c.1586-162_1586-161del | intron_variant | 1 | NM_053274.3 | P1 | |||
GLMN | ENST00000495106.5 | c.*247-162_*247-161del | intron_variant, NMD_transcript_variant | 1 | |||||
GLMN | ENST00000495852.6 | c.809-162_809-161del | intron_variant | 5 | |||||
GLMN | ENST00000471465.1 | n.532-162_532-161del | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.260 AC: 39435AN: 151776Hom.: 6472 Cov.: 23
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.260 AC: 39461AN: 151892Hom.: 6481 Cov.: 23 AF XY: 0.261 AC XY: 19390AN XY: 74208
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at