chr1-240493250-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PS1_ModerateBP4_StrongBS2
The NM_022469.4(GREM2):c.226C>G(p.Gln76Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00275 in 1,614,122 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_022469.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GREM2 | NM_022469.4 | c.226C>G | p.Gln76Glu | missense_variant | 2/2 | ENST00000318160.5 | |
GREM2 | XM_047427832.1 | c.280C>G | p.Gln94Glu | missense_variant | 3/3 | ||
GREM2 | XM_047427839.1 | c.280C>G | p.Gln94Glu | missense_variant | 4/4 | ||
GREM2 | XM_011544249.3 | c.226C>G | p.Gln76Glu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GREM2 | ENST00000318160.5 | c.226C>G | p.Gln76Glu | missense_variant | 2/2 | 1 | NM_022469.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00179 AC: 273AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00169 AC: 423AN: 250576Hom.: 2 AF XY: 0.00177 AC XY: 240AN XY: 135578
GnomAD4 exome AF: 0.00285 AC: 4159AN: 1461800Hom.: 10 Cov.: 31 AF XY: 0.00286 AC XY: 2083AN XY: 727216
GnomAD4 genome ? AF: 0.00180 AC: 274AN: 152322Hom.: 0 Cov.: 32 AF XY: 0.00164 AC XY: 122AN XY: 74498
ClinVar
Submissions by phenotype
Tooth agenesis, selective, 9 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at