NM_015132.5:c.1954-14_1954-9dupTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015132.5(SNX13):​c.1954-14_1954-9dupTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000015 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

SNX13
NM_015132.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43

Publications

0 publications found
Variant links:
Genes affected
SNX13 (HGNC:21335): (sorting nexin 13) This gene encodes a PHOX domain- and RGS domain-containing protein that belongs to the sorting nexin (SNX) family and the regulator of G protein signaling (RGS) family. The PHOX domain is a phosphoinositide binding domain, and the SNX family members are involved in intracellular trafficking. The RGS family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. The RGS domain of this protein interacts with G alpha(s), accelerates its GTP hydrolysis, and attenuates G alpha(s)-mediated signaling. Overexpression of this protein delayes lysosomal degradation of the epidermal growth factor receptor. Because of its bifunctional role, this protein may link heterotrimeric G protein signaling and vesicular trafficking. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNX13NM_015132.5 linkc.1954-14_1954-9dupTTTTTT intron_variant Intron 19 of 25 ENST00000428135.7 NP_055947.1 Q9Y5W8-2A0A024R9Z9Q86XC4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNX13ENST00000428135.7 linkc.1954-9_1954-8insTTTTTT intron_variant Intron 19 of 25 1 NM_015132.5 ENSP00000398789.2 Q9Y5W8-2
SNX13ENST00000611725.4 linkc.1987-9_1987-8insTTTTTT intron_variant Intron 19 of 24 1 ENSP00000479044.1 A0A087WUZ7
SNX13ENST00000496855.1 linkn.298-9_298-8insTTTTTT intron_variant Intron 2 of 8 1
SNX13ENST00000409076.6 linkn.*1652-9_*1652-8insTTTTTT intron_variant Intron 20 of 26 2 ENSP00000387053.2 F8W8A9

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
130360
Hom.:
0
Cov.:
0
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000146
AC:
16
AN:
1092866
Hom.:
0
Cov.:
12
AF XY:
0.0000207
AC XY:
11
AN XY:
531370
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
21030
American (AMR)
AF:
0.00
AC:
0
AN:
9690
Ashkenazi Jewish (ASJ)
AF:
0.0000584
AC:
1
AN:
17126
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24864
South Asian (SAS)
AF:
0.0000492
AC:
2
AN:
40666
European-Finnish (FIN)
AF:
0.0000644
AC:
2
AN:
31038
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4236
European-Non Finnish (NFE)
AF:
0.0000111
AC:
10
AN:
899574
Other (OTH)
AF:
0.0000224
AC:
1
AN:
44642
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.328
Heterozygous variant carriers
0
1
2
3
4
5
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
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
130360
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
62466
African (AFR)
AF:
0.00
AC:
0
AN:
36528
American (AMR)
AF:
0.00
AC:
0
AN:
12902
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3160
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4686
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4330
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
6160
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
274
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
59764
Other (OTH)
AF:
0.00
AC:
0
AN:
1776

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs34649849; hg19: chr7-17854575; API