rs458628
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032312.4(YIPF4):c.80-154G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,034 control chromosomes in the GnomAD database, including 31,213 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 0.63 ( 31213 hom., cov: 33)
Consequence
YIPF4
NM_032312.4 intron
NM_032312.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00200
Genes affected
YIPF4 (HGNC:28145): (Yip1 domain family member 4) Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport and vesicle fusion with Golgi apparatus. Located in Golgi apparatus; endoplasmic reticulum; and plasma 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=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YIPF4 | NM_032312.4 | c.80-154G>A | intron_variant | ENST00000238831.9 | |||
YIPF4 | XM_005264599.4 | c.80-154G>A | intron_variant | ||||
YIPF4 | XM_024453173.2 | c.80-154G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YIPF4 | ENST00000238831.9 | c.80-154G>A | intron_variant | 1 | NM_032312.4 | P1 | |||
YIPF4 | ENST00000437765.1 | c.5-154G>A | intron_variant, NMD_transcript_variant | 5 | |||||
YIPF4 | ENST00000495355.1 | n.107-154G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.634 AC: 96359AN: 151916Hom.: 31171 Cov.: 33
GnomAD3 genomes
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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: 0.634 AC: 96453AN: 152034Hom.: 31213 Cov.: 33 AF XY: 0.632 AC XY: 46947AN XY: 74306
GnomAD4 genome
?
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96453
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33
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46947
AN XY:
74306
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1399
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3462
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