9-109167006-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014334.4(FRRS1L):c.133C>A(p.Arg45Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000787 in 1,229,646 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014334.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRRS1L | ENST00000561981.5 | c.133C>A | p.Arg45Ser | missense_variant | 1/5 | 1 | NM_014334.4 | ENSP00000477141.2 | ||
FRRS1L | ENST00000644747.1 | n.-3C>A | upstream_gene_variant | ENSP00000493964.1 |
Frequencies
GnomAD3 genomes AF: 0.00408 AC: 608AN: 149126Hom.: 7 Cov.: 25
GnomAD3 exomes AF: 0.000523 AC: 2AN: 3826Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 2260
GnomAD4 exome AF: 0.000334 AC: 361AN: 1080422Hom.: 4 Cov.: 33 AF XY: 0.000309 AC XY: 159AN XY: 514696
GnomAD4 genome AF: 0.00407 AC: 607AN: 149224Hom.: 7 Cov.: 25 AF XY: 0.00379 AC XY: 276AN XY: 72804
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | FRRS1L: BS1, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 15, 2021 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
FRRS1L-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 14, 2024 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Developmental and epileptic encephalopathy, 37 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at