chr11-17356761-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001202439.3(NCR3LG1):c.181A>G(p.Met61Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000443 in 1,536,404 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_001202439.3 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 | UniProt |
---|---|---|---|---|---|---|---|
NCR3LG1 | NM_001202439.3 | c.181A>G | p.Met61Val | missense_variant | 2/5 | ENST00000338965.9 | |
NCR3LG1 | XM_047426906.1 | c.181A>G | p.Met61Val | missense_variant | 2/6 | ||
NCR3LG1 | XM_011520074.4 | c.94A>G | p.Met32Val | missense_variant | 2/5 | ||
NCR3LG1 | XM_011520075.4 | c.94A>G | p.Met32Val | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCR3LG1 | ENST00000338965.9 | c.181A>G | p.Met61Val | missense_variant | 2/5 | 1 | NM_001202439.3 | P1 | |
NCR3LG1 | ENST00000530403.1 | c.181A>G | p.Met61Val | missense_variant, NMD_transcript_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000107 AC: 15AN: 140644Hom.: 0 AF XY: 0.000132 AC XY: 10AN XY: 76004
GnomAD4 exome AF: 0.0000470 AC: 65AN: 1384070Hom.: 0 Cov.: 31 AF XY: 0.0000542 AC XY: 37AN XY: 682968
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152334Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.181A>G (p.M61V) alteration is located in exon 2 (coding exon 2) of the NCR3LG1 gene. This alteration results from a A to G substitution at nucleotide position 181, causing the methionine (M) at amino acid position 61 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