1-53883154-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018982.5(YIPF1):c.154G>A(p.Asp52Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000075 in 1,600,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
YIPF1
NM_018982.5 missense
NM_018982.5 missense
Scores
6
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 5.87
Genes affected
YIPF1 (HGNC:25231): (Yip1 domain family member 1) Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Located in several cellular components, including Golgi apparatus subcompartment; nucleoplasm; and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.27261764).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YIPF1 | NM_018982.5 | c.154G>A | p.Asp52Asn | missense_variant | 4/11 | ENST00000072644.7 | |
YIPF1 | NR_036639.2 | n.508G>A | non_coding_transcript_exon_variant | 4/12 | |||
YIPF1 | NR_036640.2 | n.288G>A | non_coding_transcript_exon_variant | 3/11 | |||
YIPF1 | NR_135075.2 | n.208G>A | non_coding_transcript_exon_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YIPF1 | ENST00000072644.7 | c.154G>A | p.Asp52Asn | missense_variant | 4/11 | 1 | NM_018982.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152224Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000838 AC: 2AN: 238728Hom.: 0 AF XY: 0.00000774 AC XY: 1AN XY: 129206
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GnomAD4 exome AF: 0.00000414 AC: 6AN: 1448156Hom.: 0 Cov.: 30 AF XY: 0.00000417 AC XY: 3AN XY: 720130
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GnomAD4 genome AF: 0.0000394 AC: 6AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74504
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
D
Sift4G
Benign
T
Polyphen
P
Vest4
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ClinPred
T
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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