6-85508320-TAAAAAAAA-TAA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_153816.6(SNX14):c.2654-267_2654-262delTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000649 in 770,030 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000065 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SNX14
NM_153816.6 intron
NM_153816.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.80
Publications
0 publications found
Genes affected
SNX14 (HGNC:14977): (sorting nexin 14) This gene encodes a member of the sorting nexin family. Members of this family have a phox (PX) phosphoinositide binding domain and are involved in intracellular trafficking. The encoded protein also contains a regulator of G protein signaling (RGS) domain. Regulator of G protein signaling family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. Alternate splicing results in transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]
SNX14 Gene-Disease associations (from GenCC):
- autosomal recessive spinocerebellar ataxia 20Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, G2P, Ambry Genetics, PanelApp Australia
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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_153816.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SNX14 | NM_153816.6 | MANE Select | c.2654-267_2654-262delTTTTTT | intron | N/A | NP_722523.1 | Q9Y5W7-1 | ||
| SNX14 | NM_001350532.2 | c.2717-267_2717-262delTTTTTT | intron | N/A | NP_001337461.1 | A0A804HKZ1 | |||
| SNX14 | NM_001350533.2 | c.2651-267_2651-262delTTTTTT | intron | N/A | NP_001337462.1 | A0A804HKC6 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SNX14 | ENST00000314673.8 | TSL:1 MANE Select | c.2654-267_2654-262delTTTTTT | intron | N/A | ENSP00000313121.3 | Q9Y5W7-1 | ||
| SNX14 | ENST00000369627.6 | TSL:1 | c.2627-267_2627-262delTTTTTT | intron | N/A | ENSP00000358641.2 | Q9Y5W7-4 | ||
| SNX14 | ENST00000346348.7 | TSL:1 | c.2495-267_2495-262delTTTTTT | intron | N/A | ENSP00000257769.3 | Q9Y5W7-2 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 99028Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
0
AN:
99028
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000649 AC: 50AN: 770030Hom.: 0 AF XY: 0.0000587 AC XY: 21AN XY: 357766 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
50
AN:
770030
Hom.:
AF XY:
AC XY:
21
AN XY:
357766
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
14394
American (AMR)
AF:
AC:
1
AN:
1228
Ashkenazi Jewish (ASJ)
AF:
AC:
2
AN:
5170
East Asian (EAS)
AF:
AC:
2
AN:
4348
South Asian (SAS)
AF:
AC:
0
AN:
15256
European-Finnish (FIN)
AF:
AC:
1
AN:
986
Middle Eastern (MID)
AF:
AC:
0
AN:
1568
European-Non Finnish (NFE)
AF:
AC:
43
AN:
701500
Other (OTH)
AF:
AC:
1
AN:
25580
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.267
Heterozygous variant carriers
0
6
12
18
24
30
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
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>80
Age
GnomAD4 genome 0.00 AC: 0AN: 99028Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 46986
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
99028
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
46986
African (AFR)
AF:
AC:
0
AN:
27162
American (AMR)
AF:
AC:
0
AN:
9144
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2414
East Asian (EAS)
AF:
AC:
0
AN:
3818
South Asian (SAS)
AF:
AC:
0
AN:
3274
European-Finnish (FIN)
AF:
AC:
0
AN:
4754
Middle Eastern (MID)
AF:
AC:
0
AN:
184
European-Non Finnish (NFE)
AF:
AC:
0
AN:
46298
Other (OTH)
AF:
AC:
0
AN:
1352
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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