rs7448390
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030799.9(YIPF5):c.*1458A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 981,528 control chromosomes in the GnomAD database, including 21,788 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 0.23 ( 4130 hom., cov: 30)
Exomes 𝑓: 0.20 ( 17658 hom. )
Consequence
YIPF5
NM_030799.9 3_prime_UTR
NM_030799.9 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.444
Genes affected
YIPF5 (HGNC:24877): (Yip1 domain family member 5) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; regulation of ER to Golgi vesicle-mediated transport; and vesicle fusion with Golgi apparatus. Located in Golgi apparatus; endoplasmic reticulum; and nucleoplasm. [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=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YIPF5 | NM_030799.9 | c.*1458A>G | 3_prime_UTR_variant | 6/6 | ENST00000274496.10 | ||
YIPF5 | NM_001024947.4 | c.*1458A>G | 3_prime_UTR_variant | 6/6 | |||
YIPF5 | NM_001271732.2 | c.*1458A>G | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YIPF5 | ENST00000274496.10 | c.*1458A>G | 3_prime_UTR_variant | 6/6 | 1 | NM_030799.9 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.230 AC: 34645AN: 150826Hom.: 4125 Cov.: 30
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30
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GnomAD4 exome AF: 0.203 AC: 168811AN: 830602Hom.: 17658 Cov.: 32 AF XY: 0.202 AC XY: 77587AN XY: 383854
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GnomAD4 genome ? AF: 0.230 AC: 34694AN: 150926Hom.: 4130 Cov.: 30 AF XY: 0.231 AC XY: 17005AN XY: 73762
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1133
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3432
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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