rs1897318
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001039112.2(FER1L6):c.-29G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,134 control chromosomes in the GnomAD database, including 12,529 homozygotes. 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 0.39 ( 12524 hom., cov: 32)
Exomes 𝑓: 0.55 ( 5 hom. )
Consequence
FER1L6
NM_001039112.2 5_prime_UTR
NM_001039112.2 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.594
Genes affected
FER1L6 (HGNC:28065): (fer-1 like family member 6) Predicted to enable metal ion binding activity. Predicted to be involved in plasma membrane organization. Predicted to act upstream of or within response to bacterium. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FER1L6 | NM_001039112.2 | c.-29G>A | 5_prime_UTR_variant | 1/41 | ENST00000522917.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER1L6 | ENST00000522917.5 | c.-29G>A | 5_prime_UTR_variant | 1/41 | 1 | NM_001039112.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.394 AC: 59895AN: 151974Hom.: 12525 Cov.: 32
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GnomAD4 exome AF: 0.548 AC: 23AN: 42Hom.: 5 Cov.: 0 AF XY: 0.563 AC XY: 18AN XY: 32
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GnomAD4 genome ? AF: 0.394 AC: 59903AN: 152092Hom.: 12524 Cov.: 32 AF XY: 0.388 AC XY: 28813AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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