chr6-41335881-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004828.4(NCR2):c.5C>G(p.Ala2Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000256 in 1,565,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004828.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCR2 | NM_004828.4 | c.5C>G | p.Ala2Gly | missense_variant | 1/5 | ENST00000373089.10 | |
NCR2 | NM_001199509.2 | c.5C>G | p.Ala2Gly | missense_variant | 1/6 | ||
NCR2 | NM_001199510.2 | c.5C>G | p.Ala2Gly | missense_variant | 1/6 | ||
NCR2 | XM_017011500.2 | c.29C>G | p.Ala10Gly | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCR2 | ENST00000373089.10 | c.5C>G | p.Ala2Gly | missense_variant | 1/5 | 1 | NM_004828.4 | P2 | |
NCR2 | ENST00000373086.3 | c.5C>G | p.Ala2Gly | missense_variant | 1/6 | 1 | A2 | ||
NCR2 | ENST00000373083.8 | c.5C>G | p.Ala2Gly | missense_variant | 1/6 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000664 AC: 1AN: 150676Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000559 AC: 1AN: 178900Hom.: 0 AF XY: 0.0000106 AC XY: 1AN XY: 94700
GnomAD4 exome AF: 0.00000212 AC: 3AN: 1414770Hom.: 0 Cov.: 34 AF XY: 0.00000286 AC XY: 2AN XY: 699176
GnomAD4 genome ? AF: 0.00000664 AC: 1AN: 150676Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73624
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 02, 2023 | The c.5C>G (p.A2G) alteration is located in exon 1 (coding exon 1) of the NCR2 gene. This alteration results from a C to G substitution at nucleotide position 5, causing the alanine (A) at amino acid position 2 to be replaced by a glycine (G). 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