chr5-144165488-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 2P and 14B. PM1BP4_StrongBP6_ModerateBS1BS2
The NM_030799.9(YIPF5):c.227C>T(p.Ala76Val) variant causes a missense change. The variant allele was found at a frequency of 0.021 in 1,614,122 control chromosomes in the GnomAD database, including 413 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 26 hom., cov: 32)
Exomes 𝑓: 0.022 ( 387 hom. )
Consequence
YIPF5
NM_030799.9 missense
NM_030799.9 missense
Scores
1
16
Clinical Significance
Conservation
PhyloP100: 4.80
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.
PM1
?
In a topological_domain Cytoplasmic (size 123) in uniprot entity YIPF5_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in NM_030799.9
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004816413).
BP6
?
Variant 5-144165488-G-A is Benign according to our data. Variant chr5-144165488-G-A is described in ClinVar as [Benign]. Clinvar id is 2655875.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0149 (2264/152276) while in subpopulation NFE AF= 0.0245 (1667/68014). AF 95% confidence interval is 0.0235. There are 26 homozygotes in gnomad4. There are 1000 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 26 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YIPF5 | NM_030799.9 | c.227C>T | p.Ala76Val | missense_variant | 3/6 | ENST00000274496.10 | |
YIPF5 | NM_001024947.4 | c.227C>T | p.Ala76Val | missense_variant | 3/6 | ||
YIPF5 | NM_001271732.2 | c.65C>T | p.Ala22Val | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YIPF5 | ENST00000274496.10 | c.227C>T | p.Ala76Val | missense_variant | 3/6 | 1 | NM_030799.9 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0149 AC: 2261AN: 152158Hom.: 26 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0141 AC: 3555AN: 251470Hom.: 38 AF XY: 0.0146 AC XY: 1981AN XY: 135906
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GnomAD4 exome AF: 0.0217 AC: 31662AN: 1461846Hom.: 387 Cov.: 31 AF XY: 0.0212 AC XY: 15431AN XY: 727226
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GnomAD4 genome ? AF: 0.0149 AC: 2264AN: 152276Hom.: 26 Cov.: 32 AF XY: 0.0134 AC XY: 1000AN XY: 74466
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114
ESP6500AA
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ESP6500EA
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196
ExAC
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Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | YIPF5: BP4, BS1, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;.;.;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;.
Polyphen
B;B;.;.;.
Vest4
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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