rs11954744
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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.611+379A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,222 control chromosomes in the GnomAD database, including 1,937 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 0.15 ( 1937 hom., cov: 31)
Consequence
YIPF5
NM_030799.9 intron
NM_030799.9 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.17
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=-0.8).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YIPF5 | NM_030799.9 | c.611+379A>T | intron_variant | ENST00000274496.10 | NP_110426.4 | |||
YIPF5 | NM_001024947.4 | c.611+379A>T | intron_variant | NP_001020118.1 | ||||
YIPF5 | NM_001271732.2 | c.449+379A>T | intron_variant | NP_001258661.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YIPF5 | ENST00000274496.10 | c.611+379A>T | intron_variant | 1 | NM_030799.9 | ENSP00000274496.5 | ||||
YIPF5 | ENST00000448443.6 | c.611+379A>T | intron_variant | 1 | ENSP00000397704.2 | |||||
YIPF5 | ENST00000513112.5 | c.449+379A>T | intron_variant | 1 | ENSP00000425422.1 | |||||
YIPF5 | ENST00000519064.5 | c.449+379A>T | intron_variant | 2 | ENSP00000429777.1 |
Frequencies
GnomAD3 genomes AF: 0.153 AC: 23240AN: 152104Hom.: 1934 Cov.: 31
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.153 AC: 23248AN: 152222Hom.: 1937 Cov.: 31 AF XY: 0.152 AC XY: 11300AN XY: 74406
GnomAD4 genome
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31
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293
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3478
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