12-69574113-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001278356.2(FRS2):āc.685A>Gā(p.Lys229Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,614,058 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001278356.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRS2 | NM_001278356.2 | c.685A>G | p.Lys229Glu | missense_variant | 9/9 | ENST00000549921.6 | NP_001265285.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRS2 | ENST00000549921.6 | c.685A>G | p.Lys229Glu | missense_variant | 9/9 | 1 | NM_001278356.2 | ENSP00000450048.1 | ||
FRS2 | ENST00000550389.5 | c.685A>G | p.Lys229Glu | missense_variant | 7/7 | 1 | ENSP00000447241.1 | |||
FRS2 | ENST00000397997.6 | c.685A>G | p.Lys229Glu | missense_variant | 7/7 | 5 | ENSP00000381083.2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152274Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249500Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135364
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461784Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727212
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152274Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74404
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2024 | The c.685A>G (p.K229E) alteration is located in exon 10 (coding exon 5) of the FRS2 gene. This alteration results from a A to G substitution at nucleotide position 685, causing the lysine (K) at amino acid position 229 to be replaced by a glutamic acid (E). 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