rs34637446
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP3BS1
The NM_001166355.2(LFNG):c.155_166delGATGGATGGATG(p.Gly52_Asp55del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 1,584,326 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000060 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000084 ( 0 hom. )
Consequence
LFNG
NM_001166355.2 disruptive_inframe_deletion
NM_001166355.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.46
Genes affected
LFNG (HGNC:6560): (LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase) This gene is a member of the glycosyltransferase 31 gene family. Members of this gene family, which also includes the MFNG (GeneID: 4242) and RFNG (GeneID: 5986) genes, encode evolutionarily conserved glycosyltransferases that act in the Notch signaling pathway to define boundaries during embryonic development. While their genomic structure is distinct from other glycosyltransferases, these proteins have a fucose-specific beta-1,3-N-acetylglucosaminyltransferase activity that leads to elongation of O-linked fucose residues on Notch, which alters Notch signaling. The protein encoded by this gene is predicted to be a single-pass type II Golgi membrane protein but it may also be secreted and proteolytically processed like the related proteins in mouse and Drosophila (PMID: 9187150). Mutations in this gene have been associated with autosomal recessive spondylocostal dysostosis 3. [provided by RefSeq, May 2018]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_001166355.2
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000595 (9/151232) while in subpopulation EAS AF= 0.000197 (1/5088). AF 95% confidence interval is 0.0000795. There are 0 homozygotes in gnomad4. There are 1 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
Transcripts
RefSeq
Ensembl
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GnomAD3 genomes 0.0000596 AC: 9AN: 151116Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000837 AC: 12AN: 1433094Hom.: 0 AF XY: 0.00000701 AC XY: 5AN XY: 713272
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GnomAD4 genome 0.0000595 AC: 9AN: 151232Hom.: 0 Cov.: 0 AF XY: 0.0000135 AC XY: 1AN XY: 73834
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at