10-94334687-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022451.11(NOC3L):āc.2221A>Gā(p.Met741Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000893 in 1,613,226 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022451.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOC3L | NM_022451.11 | c.2221A>G | p.Met741Val | missense_variant | 20/21 | ENST00000371361.3 | NP_071896.8 | |
NOC3L | XR_002957007.2 | n.2322A>G | non_coding_transcript_exon_variant | 20/22 | ||||
NOC3L | XR_007061982.1 | n.2322A>G | non_coding_transcript_exon_variant | 20/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOC3L | ENST00000371361.3 | c.2221A>G | p.Met741Val | missense_variant | 20/21 | 1 | NM_022451.11 | ENSP00000360412.3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000759 AC: 19AN: 250450Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135438
GnomAD4 exome AF: 0.0000931 AC: 136AN: 1461038Hom.: 1 Cov.: 30 AF XY: 0.0000881 AC XY: 64AN XY: 726818
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.2221A>G (p.M741V) alteration is located in exon 20 (coding exon 20) of the NOC3L gene. This alteration results from a A to G substitution at nucleotide position 2221, causing the methionine (M) at amino acid position 741 to be replaced by a valine (V). 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