rs9727115

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015976.5(SNX7):​c.1125+9794G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,016 control chromosomes in the GnomAD database, including 10,390 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 10390 hom., cov: 32)

Consequence

SNX7
NM_015976.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.531

Publications

17 publications found
Variant links:
Genes affected
SNX7 (HGNC:14971): (sorting nexin 7) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region like some family members, and its exact function is unknown. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 11. [provided by RefSeq, Jun 2010]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNX7NM_015976.5 linkc.1125+9794G>A intron_variant Intron 7 of 8 ENST00000306121.8 NP_057060.2 Q9UNH6-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNX7ENST00000306121.8 linkc.1125+9794G>A intron_variant Intron 7 of 8 1 NM_015976.5 ENSP00000304429.3 Q9UNH6-3
SNX7ENST00000528824.1 linkn.*945+9794G>A intron_variant Intron 8 of 8 1 ENSP00000435172.1 E9PLE1
SNX7ENST00000529992.5 linkc.960+9794G>A intron_variant Intron 6 of 7 2 ENSP00000434731.1 E9PNL2

Frequencies

GnomAD3 genomes
AF:
0.366
AC:
55618
AN:
151898
Hom.:
10387
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.407
Gnomad AMI
AF:
0.293
Gnomad AMR
AF:
0.356
Gnomad ASJ
AF:
0.418
Gnomad EAS
AF:
0.397
Gnomad SAS
AF:
0.320
Gnomad FIN
AF:
0.309
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.351
Gnomad OTH
AF:
0.391
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.366
AC:
55633
AN:
152016
Hom.:
10390
Cov.:
32
AF XY:
0.362
AC XY:
26910
AN XY:
74288
show subpopulations
African (AFR)
AF:
0.407
AC:
16859
AN:
41462
American (AMR)
AF:
0.355
AC:
5425
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
0.418
AC:
1452
AN:
3470
East Asian (EAS)
AF:
0.398
AC:
2050
AN:
5152
South Asian (SAS)
AF:
0.319
AC:
1539
AN:
4822
European-Finnish (FIN)
AF:
0.309
AC:
3268
AN:
10572
Middle Eastern (MID)
AF:
0.373
AC:
109
AN:
292
European-Non Finnish (NFE)
AF:
0.351
AC:
23841
AN:
67956
Other (OTH)
AF:
0.390
AC:
824
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1808
3615
5423
7230
9038
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
536
1072
1608
2144
2680
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.361
Hom.:
20048
Bravo
AF:
0.369
Asia WGS
AF:
0.387
AC:
1347
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.0
DANN
Benign
0.67
PhyloP100
0.53
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs9727115; hg19: chr1-99177253; API