chr12-69570412-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001278356.2(FRS2):c.148C>T(p.Arg50Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000323 in 1,612,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R50H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001278356.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRS2 | NM_001278356.2 | c.148C>T | p.Arg50Cys | missense_variant | 6/9 | ENST00000549921.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRS2 | ENST00000549921.6 | c.148C>T | p.Arg50Cys | missense_variant | 6/9 | 1 | NM_001278356.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249536Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135390
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1460230Hom.: 0 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 726598
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.148C>T (p.R50C) alteration is located in exon 7 (coding exon 2) of the FRS2 gene. This alteration results from a C to T substitution at nucleotide position 148, causing the arginine (R) at amino acid position 50 to be replaced by a cysteine (C). 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