rs13088281
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_052859.4(RFT1):c.697-1652G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 152,254 control chromosomes in the GnomAD database, including 565 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 0.078 ( 565 hom., cov: 33)
Consequence
RFT1
NM_052859.4 intron
NM_052859.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.03
Genes affected
RFT1 (HGNC:30220): (RFT1 homolog) This gene encodes an enzyme which catalyzes the translocation of the Man(5)GlcNAc (2)-PP-Dol intermediate from the cytoplasmic to the luminal side of the endoplasmic reticulum membrane in the pathway for the N-glycosylation of proteins. Mutations in this gene are associated with congenital disorder of glycosylation type In.[provided by RefSeq, Dec 2008]
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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=-0.77).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RFT1 | NM_052859.4 | c.697-1652G>T | intron_variant | ENST00000296292.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFT1 | ENST00000296292.8 | c.697-1652G>T | intron_variant | 1 | NM_052859.4 | P1 | |||
RFT1 | ENST00000394738.7 | c.580-1652G>T | intron_variant | 5 | |||||
RFT1 | ENST00000467048.1 | c.559-1652G>T | intron_variant | 3 | |||||
RFT1 | ENST00000471158.1 | n.139-1652G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0777 AC: 11821AN: 152136Hom.: 561 Cov.: 33
GnomAD3 genomes
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11821
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152136
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0777 AC: 11829AN: 152254Hom.: 565 Cov.: 33 AF XY: 0.0770 AC XY: 5730AN XY: 74426
GnomAD4 genome
?
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11829
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152254
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33
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5730
AN XY:
74426
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315
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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