6-41771220-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006653.5(FRS3):c.878G>A(p.Gly293Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000375 in 1,573,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006653.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FRS3 | NM_006653.5 | c.878G>A | p.Gly293Glu | missense_variant | Exon 7 of 7 | ENST00000373018.7 | NP_006644.1 | |
FRS3 | XM_011514254.2 | c.878G>A | p.Gly293Glu | missense_variant | Exon 7 of 7 | XP_011512556.1 | ||
FRS3 | XM_047418097.1 | c.878G>A | p.Gly293Glu | missense_variant | Exon 8 of 8 | XP_047274053.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000121 AC: 27AN: 222534Hom.: 0 AF XY: 0.000118 AC XY: 14AN XY: 118556
GnomAD4 exome AF: 0.0000324 AC: 46AN: 1421174Hom.: 0 Cov.: 33 AF XY: 0.0000328 AC XY: 23AN XY: 701252
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.878G>A (p.G293E) alteration is located in exon 7 (coding exon 5) of the FRS3 gene. This alteration results from a G to A substitution at nucleotide position 878, causing the glycine (G) at amino acid position 293 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