rs1045481
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_015721.3(GEMIN4):c.3126C>T(p.Ile1042Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 1,613,264 control chromosomes in the GnomAD database, including 46,642 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_015721.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GEMIN4 | ENST00000319004.6 | c.3126C>T | p.Ile1042Ile | synonymous_variant | Exon 2 of 2 | 1 | NM_015721.3 | ENSP00000321706.5 | ||
GEMIN4 | ENST00000576778.1 | c.3093C>T | p.Ile1031Ile | synonymous_variant | Exon 1 of 1 | 6 | ENSP00000459565.1 |
Frequencies
GnomAD3 genomes AF: 0.191 AC: 29026AN: 152152Hom.: 3259 Cov.: 34
GnomAD3 exomes AF: 0.204 AC: 50474AN: 247916Hom.: 5637 AF XY: 0.208 AC XY: 28034AN XY: 134660
GnomAD4 exome AF: 0.239 AC: 349395AN: 1460994Hom.: 43381 Cov.: 32 AF XY: 0.238 AC XY: 173113AN XY: 726764
GnomAD4 genome AF: 0.191 AC: 29033AN: 152270Hom.: 3261 Cov.: 34 AF XY: 0.189 AC XY: 14066AN XY: 74464
ClinVar
Submissions by phenotype
GEMIN4-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at