chr15-64151822-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_024798.3(SNX22):c.47C>T(p.Pro16Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SNX22
NM_024798.3 missense
NM_024798.3 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: 2.98
Publications
0 publications found
Genes affected
SNX22 (HGNC:16315): (sorting nexin 22) The protein encoded by this gene is a sorting nexin that is found in the cytoplasm, where it interacts with membrane-bound phosphatidylinositol 3-phosphate. The encoded protein may play a role in intracellular trafficking. Two transcript variants, one protein-coding and the other not protein-coding, have been found for this gene. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_024798.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SNX22 | TSL:1 MANE Select | c.47C>T | p.Pro16Leu | missense | Exon 1 of 7 | ENSP00000323435.4 | Q96L94-1 | ||
| SNX22 | TSL:1 | n.79C>T | non_coding_transcript_exon | Exon 1 of 4 | |||||
| SNX22 | c.47C>T | p.Pro16Leu | missense | Exon 1 of 6 | ENSP00000568264.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00 AC: 0AN: 129990 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
129990
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1386166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 683898
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1386166
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
683898
African (AFR)
AF:
AC:
0
AN:
30098
American (AMR)
AF:
AC:
0
AN:
35088
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24854
East Asian (EAS)
AF:
AC:
0
AN:
34878
South Asian (SAS)
AF:
AC:
0
AN:
77722
European-Finnish (FIN)
AF:
AC:
0
AN:
44134
Middle Eastern (MID)
AF:
AC:
0
AN:
5412
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1076354
Other (OTH)
AF:
AC:
0
AN:
57626
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ExAC
AF:
AC:
1
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of glycosylation at P16 (P = 0.0422)
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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