Variant rs35296149 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015976.5(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
NM_015976.5 missense

Scores

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]

SNX7 links:

SNX7 (HGNC:):

SNX7 links:

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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
SNX7	NM_015976.5 linkuse as main transcript	c.367T>A	p.Ser123Thr	missense_variant	3/9	ENST00000306121.8	NP_057060.2	Q9UNH6-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX7	ENST00000306121.8 linkuse as main transcript	c.367T>A	p.Ser123Thr	missense_variant	3/9	1	NM_015976.5	ENSP00000304429.3		Q9UNH6-3

Frequencies

GnomAD3 genomes

AF:

0.0319

AC:

4845

AN:

152036

Hom.:

373

Cov.:

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.:

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.:

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:

ALSPAC

AF:

0.0127

AC:

ESP6500AA

AF:

0.0138

AC:

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

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.29

DEOGEN2

Benign

0.0058

T;.;T

Eigen

Benign

-0.73

Eigen_PC

Benign

-0.42

FATHMM_MKL

Uncertain

0.82

LIST_S2

Benign

0.65

T;T;T

MetaRNN

Benign

0.0012

T;T;T

MetaSVM

Benign

-0.96

PrimateAI

Uncertain

0.59

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

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over