1-946207-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015658.4(NOC2L):c.1883G>A(p.Arg628Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000248 in 1,613,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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.1883G>A | p.Arg628Gln | missense_variant | Exon 16 of 19 | 1 | NM_015658.4 | ENSP00000317992.6 | ||
NOC2L | ENST00000477976.5 | n.3330G>A | non_coding_transcript_exon_variant | Exon 14 of 17 | 5 | |||||
NOC2L | ENST00000483767.5 | n.739G>A | non_coding_transcript_exon_variant | Exon 2 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152244Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000200 AC: 50AN: 250622Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135592
GnomAD4 exome AF: 0.000248 AC: 362AN: 1460952Hom.: 0 Cov.: 30 AF XY: 0.000227 AC XY: 165AN XY: 726652
GnomAD4 genome AF: 0.000249 AC: 38AN: 152362Hom.: 0 Cov.: 34 AF XY: 0.000309 AC XY: 23AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1883G>A (p.R628Q) alteration is located in exon 16 (coding exon 16) of the NOC2L gene. This alteration results from a G to A substitution at nucleotide position 1883, causing the arginine (R) at amino acid position 628 to be replaced by a glutamine (Q). 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