rs560644274
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The 9-109167260-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000482 in 1,245,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 28)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FRRS1L
NM_014334.4 upstream_gene
NM_014334.4 upstream_gene
Scores
1
1
14
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.16
Genes affected
FRRS1L (HGNC:1362): (ferric chelate reductase 1 like) This gene encodes a component of the outer-core of an alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor protein in the brain. The encoded protein is thought to interact with inner-core components of the receptor, and play a role in the modulation of glutamate signaling. Mutations in this gene are associated with early infantile epileptic encephalopathy 37. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.21279296).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRRS1L | NM_014334.4 | upstream_gene_variant | ENST00000561981.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRRS1L | ENST00000561981.5 | upstream_gene_variant | 1 | NM_014334.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 150650Hom.: 0 Cov.: 28 FAILED QC
GnomAD3 genomes
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150650
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28
FAILED QC
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GnomAD3 exomes AF: 0.0000129 AC: 1AN: 77634Hom.: 0 AF XY: 0.0000229 AC XY: 1AN XY: 43750
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GnomAD4 exome AF: 0.00000482 AC: 6AN: 1245412Hom.: 0 Cov.: 25 AF XY: 0.00000653 AC XY: 4AN XY: 612886
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00000664 AC: 1AN: 150650Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 73482
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Pathogenic
D
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of phosphorylation at S14 (P = 0.2239);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at