rs35296149

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000306121.8(SNX7):​c.367T>A​(p.Ser123Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 1,600,472 control chromosomes in the GnomAD database, including 3,594 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.032 ( 377 hom., cov: 32)
Exomes 𝑓: 0.027 ( 3217 hom. )

Consequence

SNX7
ENST00000306121.8 missense

Scores

2
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.70
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0012304187).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SNX7NM_015976.5 linkuse as main transcriptc.367T>A p.Ser123Thr missense_variant 3/9 ENST00000306121.8 NP_057060.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SNX7ENST00000306121.8 linkuse as main transcriptc.367T>A p.Ser123Thr missense_variant 3/91 NM_015976.5 ENSP00000304429 P1Q9UNH6-3
SNX7ENST00000528824.1 linkuse as main transcriptc.*187T>A 3_prime_UTR_variant, NMD_transcript_variant 4/91 ENSP00000435172
SNX7ENST00000529992.5 linkuse as main transcriptc.367T>A p.Ser123Thr missense_variant 3/82 ENSP00000434731
SNX7ENST00000454199.1 linkuse as main transcriptc.175T>A p.Ser59Thr missense_variant 3/44 ENSP00000388266

Frequencies

GnomAD3 genomes
AF:
0.0319
AC:
4845
AN:
152036
Hom.:
373
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0149
Gnomad AMI
AF:
0.0318
Gnomad AMR
AF:
0.0691
Gnomad ASJ
AF:
0.00894
Gnomad EAS
AF:
0.342
Gnomad SAS
AF:
0.0552
Gnomad FIN
AF:
0.0239
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0113
Gnomad OTH
AF:
0.0273
GnomAD3 exomes
AF:
0.0586
AC:
14413
AN:
245792
Hom.:
1518
AF XY:
0.0527
AC XY:
7010
AN XY:
133140
show subpopulations
Gnomad AFR exome
AF:
0.0150
Gnomad AMR exome
AF:
0.144
Gnomad ASJ exome
AF:
0.00914
Gnomad EAS exome
AF:
0.347
Gnomad SAS exome
AF:
0.0397
Gnomad FIN exome
AF:
0.0222
Gnomad NFE exome
AF:
0.0115
Gnomad OTH exome
AF:
0.0352
GnomAD4 exome
AF:
0.0267
AC:
38674
AN:
1448318
Hom.:
3217
Cov.:
29
AF XY:
0.0264
AC XY:
19042
AN XY:
721026
show subpopulations
Gnomad4 AFR exome
AF:
0.0158
Gnomad4 AMR exome
AF:
0.135
Gnomad4 ASJ exome
AF:
0.0102
Gnomad4 EAS exome
AF:
0.349
Gnomad4 SAS exome
AF:
0.0393
Gnomad4 FIN exome
AF:
0.0215
Gnomad4 NFE exome
AF:
0.0108
Gnomad4 OTH exome
AF:
0.0319
GnomAD4 genome
AF:
0.0320
AC:
4864
AN:
152154
Hom.:
377
Cov.:
32
AF XY:
0.0355
AC XY:
2642
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.0150
Gnomad4 AMR
AF:
0.0700
Gnomad4 ASJ
AF:
0.00894
Gnomad4 EAS
AF:
0.342
Gnomad4 SAS
AF:
0.0560
Gnomad4 FIN
AF:
0.0239
Gnomad4 NFE
AF:
0.0113
Gnomad4 OTH
AF:
0.0284
Alfa
AF:
0.0223
Hom.:
215
Bravo
AF:
0.0387
TwinsUK
AF:
0.0127
AC:
47
ALSPAC
AF:
0.0127
AC:
49
ESP6500AA
AF:
0.0138
AC:
61
ESP6500EA
AF:
0.0127
AC:
109
ExAC
AF:
0.0552
AC:
6705
Asia WGS
AF:
0.158
AC:
549
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.66
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
13
DANN
Benign
0.29
DEOGEN2
Benign
0.0058
T;.;T
Eigen
Benign
-0.73
Eigen_PC
Benign
-0.42
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Benign
0.65
T;T;T
MetaRNN
Benign
0.0012
T;T;T
MetaSVM
Benign
-0.96
T
MutationTaster
Benign
0.00065
P;P;P
PrimateAI
Uncertain
0.59
T
PROVEAN
Benign
1.5
N;N;N
REVEL
Benign
0.053
Sift
Benign
1.0
T;T;T
Sift4G
Benign
1.0
T;T;T
Polyphen
0.027
B;B;.
Vest4
0.16
MPC
0.080
ClinPred
0.013
T
GERP RS
3.6
gMVP
0.30

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35296149; hg19: chr1-99156634; COSMIC: COSV60266548; API