NM_018946.4:c.16_21delGAGCTG
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PM4BS1_Supporting
The NM_018946.4(NANS):c.16_21delGAGCTG(p.Glu6_Leu7del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000205 in 1,610,690 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_018946.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NANS | ENST00000210444.6 | c.16_21delGAGCTG | p.Glu6_Leu7del | conservative_inframe_deletion | Exon 1 of 6 | 1 | NM_018946.4 | ENSP00000210444.5 | ||
NANS | ENST00000480925.1 | n.55_60delGAGCTG | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
NANS | ENST00000495319.1 | n.57_62delGAGCTG | non_coding_transcript_exon_variant | Exon 1 of 5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152104Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000819 AC: 2AN: 244248Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133370
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1458586Hom.: 0 AF XY: 0.0000165 AC XY: 12AN XY: 725734
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152104Hom.: 0 Cov.: 34 AF XY: 0.000108 AC XY: 8AN XY: 74294
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.16_21delGAGCTG (p.E6_L7del) alteration is located in exon 1 (coding exon 1) of the NANS gene. This alteration consists of an in-frame deletion of 6 nucleotides between nucleotide positions c.16 and c.21, resulting in the deletion of <NA> residues. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
This variant, c.16_21del, results in the deletion of 2 amino acid(s) of the NANS protein (p.Glu6_Leu7del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs776860726, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with NANS-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Spondyloepimetaphyseal dysplasia, Genevieve type Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at