chr1-53878694-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018982.5(YIPF1):āc.224C>Gā(p.Pro75Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000877 in 1,597,094 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000053 ( 0 hom., cov: 32)
Exomes š: 0.0000042 ( 0 hom. )
Consequence
YIPF1
NM_018982.5 missense
NM_018982.5 missense
Scores
5
4
10
Clinical Significance
Conservation
PhyloP100: 8.70
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 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YIPF1 | NM_018982.5 | c.224C>G | p.Pro75Arg | missense_variant | 5/11 | ENST00000072644.7 | |
YIPF1 | NR_036639.2 | n.578C>G | non_coding_transcript_exon_variant | 5/12 | |||
YIPF1 | NR_036640.2 | n.358C>G | non_coding_transcript_exon_variant | 4/11 | |||
YIPF1 | NR_135075.2 | n.278C>G | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YIPF1 | ENST00000072644.7 | c.224C>G | p.Pro75Arg | missense_variant | 5/11 | 1 | NM_018982.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000431 AC: 1AN: 232260Hom.: 0 AF XY: 0.00000793 AC XY: 1AN XY: 126138
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GnomAD4 exome AF: 0.00000415 AC: 6AN: 1444928Hom.: 0 Cov.: 31 AF XY: 0.00000417 AC XY: 3AN XY: 718994
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GnomAD4 genome AF: 0.0000526 AC: 8AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74342
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2021 | The c.224C>G (p.P75R) alteration is located in exon 5 (coding exon 3) of the YIPF1 gene. This alteration results from a C to G substitution at nucleotide position 224, causing the proline (P) at amino acid position 75 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of glycosylation at P75 (P = 0.0258);
MVP
MPC
ClinPred
D
GERP RS
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