1-945099-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015658.4(NOC2L):c.2101G>A(p.Glu701Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,613,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015658.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOC2L | ENST00000327044.7 | c.2101G>A | p.Glu701Lys | missense_variant | Exon 18 of 19 | 1 | NM_015658.4 | ENSP00000317992.6 | ||
NOC2L | ENST00000477976.5 | n.3548G>A | non_coding_transcript_exon_variant | Exon 16 of 17 | 5 | |||||
NOC2L | ENST00000483767.5 | n.957G>A | non_coding_transcript_exon_variant | Exon 4 of 5 | 2 | |||||
NOC2L | ENST00000496938.1 | n.*220G>A | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152238Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247292Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134066
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461512Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727058
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152238Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2101G>A (p.E701K) alteration is located in exon 18 (coding exon 18) of the NOC2L gene. This alteration results from a G to A substitution at nucleotide position 2101, causing the glutamic acid (E) at amino acid position 701 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at