rs560644274
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014334.4(FRRS1L):c.-122C>T 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
Consequence
NM_014334.4 upstream_gene
Scores
Clinical Significance
Conservation
Publications
- developmental and epileptic encephalopathy, 37Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- autosomal recessive non-syndromic intellectual disabilityInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014334.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FRRS1L | NM_014334.4 | MANE Select | c.-122C>T | upstream_gene | N/A | NP_055149.3 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FRRS1L | ENST00000561981.5 | TSL:1 MANE Select | c.-122C>T | upstream_gene | N/A | ENSP00000477141.2 |
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150650Hom.: 0 Cov.: 28 show subpopulations
GnomAD2 exomes AF: 0.0000129 AC: 1AN: 77634 AF XY: 0.0000229 show subpopulations
GnomAD4 exome AF: 0.00000482 AC: 6AN: 1245412Hom.: 0 Cov.: 25 AF XY: 0.00000653 AC XY: 4AN XY: 612886 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
Age Distribution
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 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at