chr1-99719644-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001361041.2(FRRS1):c.1010G>A(p.Arg337Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000589 in 1,528,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001361041.2 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 | UniProt |
---|---|---|---|---|---|---|---|
FRRS1 | NM_001361041.2 | c.1010G>A | p.Arg337Gln | missense_variant | 10/17 | ENST00000646001.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRRS1 | ENST00000646001.2 | c.1010G>A | p.Arg337Gln | missense_variant | 10/17 | NM_001361041.2 | P1 | ||
FRRS1 | ENST00000287474.9 | c.1010G>A | p.Arg337Gln | missense_variant | 10/17 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151926Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000415 AC: 1AN: 240692Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129892
GnomAD4 exome AF: 0.00000508 AC: 7AN: 1376768Hom.: 0 Cov.: 23 AF XY: 0.00000290 AC XY: 2AN XY: 689326
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151926Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74196
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2023 | The c.1010G>A (p.R337Q) alteration is located in exon 10 (coding exon 8) of the FRRS1 gene. This alteration results from a G to A substitution at nucleotide position 1010, causing the arginine (R) at amino acid position 337 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