19-34300862-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014686.5(GARRE1):c.389G>A(p.Arg130Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,400 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R130W) has been classified as Uncertain significance.
Frequency
Consequence
NM_014686.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GARRE1 | NM_014686.5 | c.389G>A | p.Arg130Gln | missense_variant | 2/14 | ENST00000299505.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GARRE1 | ENST00000299505.8 | c.389G>A | p.Arg130Gln | missense_variant | 2/14 | 1 | NM_014686.5 | P1 | |
GARRE1 | ENST00000588470.5 | c.17G>A | p.Arg6Gln | missense_variant | 3/4 | 5 | |||
GARRE1 | ENST00000588338.6 | n.263+939G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250560Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135550
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461186Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726958
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.389G>A (p.R130Q) alteration is located in exon 2 (coding exon 1) of the KIAA0355 gene. This alteration results from a G to A substitution at nucleotide position 389, causing the arginine (R) at amino acid position 130 to be replaced by a glutamine (Q). 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