rs755927285
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001130009.3(GEN1):c.1202G>A(p.Arg401Gln) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000554 in 1,445,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130009.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GEN1 | NM_001130009.3 | c.1202G>A | p.Arg401Gln | missense_variant, splice_region_variant | 11/14 | ENST00000381254.7 | |
LOC105373449 | XR_939762.3 | n.409-9754C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GEN1 | ENST00000381254.7 | c.1202G>A | p.Arg401Gln | missense_variant, splice_region_variant | 11/14 | 5 | NM_001130009.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000828 AC: 2AN: 241418Hom.: 0 AF XY: 0.00000767 AC XY: 1AN XY: 130414
GnomAD4 exome AF: 0.00000554 AC: 8AN: 1445262Hom.: 0 Cov.: 29 AF XY: 0.00000557 AC XY: 4AN XY: 718728
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | University of Washington Department of Laboratory Medicine, University of Washington | Nov 20, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at