20-5190182-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003818.4(CDS2):c.1286G>A(p.Arg429Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,804 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003818.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDS2 | NM_003818.4 | c.1286G>A | p.Arg429Gln | missense_variant | 13/13 | ENST00000460006.6 | NP_003809.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDS2 | ENST00000460006.6 | c.1286G>A | p.Arg429Gln | missense_variant | 13/13 | 1 | NM_003818.4 | ENSP00000419879 | P1 | |
CDS2 | ENST00000379070.3 | n.1541G>A | non_coding_transcript_exon_variant | 10/10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152028Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251162Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135740
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727186
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152028Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74250
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 21, 2023 | The c.1286G>A (p.R429Q) alteration is located in exon 13 (coding exon 13) of the CDS2 gene. This alteration results from a G to A substitution at nucleotide position 1286, causing the arginine (R) at amino acid position 429 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