Variant 8-81801580-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_152836.3(SNX16):c.952C>A(p.Pro318Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000094 ( 0 hom., cov: 30)

Exomes 𝑓: 0.000021 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SNX16
NM_152836.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0240

Variant links:

Genes affected

SNX16 (HGNC:14980): (sorting nexin 16) 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. The protein encoded by this gene associates with late endosome membranes as is involved in tubule formation, cholesterol transport, and transport of tetraspanin CD81. The encoded protein also inhibits cell migration and tumorigenesis. [provided by RefSeq, Jan 2017]

SNX16 links:

SNX16 (HGNC:):

SNX16 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.03828779).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX16	NM_152836.3 linkuse as main transcript	c.952C>A	p.Pro318Thr	missense_variant	8/8	ENST00000345957.9	NP_690049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SNX16	ENST00000345957.9 linkuse as main transcript	c.952C>A	p.Pro318Thr	missense_variant	8/8	1	NM_152836.3	ENSP00000322652.4	P57768-1
SNX16	ENST00000353788.8 linkuse as main transcript	c.865C>A	p.Pro289Thr	missense_variant	7/7	1		ENSP00000322631.4	P57768-2
SNX16	ENST00000396330.6 linkuse as main transcript	c.952C>A	p.Pro318Thr	missense_variant	9/9	5		ENSP00000379621.2	P57768-1
ENSG00000253334	ENST00000524337.1 linkuse as main transcript	n.103+9655G>T		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0000864

AC:

AN:

127298

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000232

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000179

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000175

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000146

AC:

AN:

205636

Hom.:

AF XY:

0.00000885

AC XY:

AN XY:

113056

show subpopulations

Gnomad AFR exome

AF:

0.0000710

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000663

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000202

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000206

AC:

AN:

1262146

Hom.:

Cov.:

AF XY:

0.0000221

AC XY:

AN XY:

633734

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000262

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000581

Gnomad4 SAS exome

AF:

0.0000260

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000207

Gnomad4 OTH exome

AF:

0.0000191

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000942

AC:

AN:

127330

Hom.:

Cov.:

AF XY:

0.000117

AC XY:

AN XY:

59962

show subpopulations

Gnomad4 AFR

AF:

0.000261

Gnomad4 AMR

AF:

0.000179

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000175

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 19, 2023

The c.952C>A (p.P318T) alteration is located in exon 9 (coding exon 7) of the SNX16 gene. This alteration results from a C to A substitution at nucleotide position 952, causing the proline (P) at amino acid position 318 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.064

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.53

DEOGEN2

Benign

0.015

.;T;T;T

Eigen

Benign

-0.89

Eigen_PC

Benign

-0.87

FATHMM_MKL

Benign

0.048

LIST_S2

Benign

0.66

T;T;T;.

M_CAP

Benign

0.011

MetaRNN

Benign

0.038

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.8

.;L;.;L

PrimateAI

Benign

0.22

PROVEAN

Benign

-1.2

N;N;.;N

REVEL

Benign

0.021

Sift

Benign

0.19

T;T;.;T

Sift4G

Benign

0.74

T;T;T;T

Polyphen

0.0

.;B;.;B

Vest4

0.044

MutPred

0.24

.;Loss of catalytic residue at P318 (P = 0.0056);.;Loss of catalytic residue at P318 (P = 0.0056);

MVP

0.40

MPC

0.27

ClinPred

0.018

GERP RS

0.22

Varity_R

0.051

gMVP

0.084

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over