6-157901963-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_016224.5(SNX9):​c.538G>A​(p.Asp180Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,613,460 control chromosomes in the GnomAD database, including 134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0074 ( 7 hom., cov: 31)
Exomes 𝑓: 0.011 ( 127 hom. )

Consequence

SNX9
NM_016224.5 missense

Scores

1
2
15

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 8.72
Variant links:
Genes affected
SNX9 (HGNC:14973): (sorting nexin 9) This gene encodes a member of the sorting nexin family. Members of this family contain a phosphoinositide binding domain, and are involved in intracellular trafficking. The encoded protein does not contain a coiled coil region, like some family members, but does contain a SRC homology domain near its N-terminus. The encoded protein is reported to have a variety of interaction partners, including of adaptor protein 2 , dynamin, tyrosine kinase non-receptor 2, Wiskott-Aldrich syndrome-like, and ARP3 actin-related protein 3. The encoded protein is implicated in several stages of intracellular trafficking, including endocytosis, macropinocytosis, and F-actin nucleation. [provided by RefSeq, Jul 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.004186243).
BP6
Variant 6-157901963-G-A is Benign according to our data. Variant chr6-157901963-G-A is described in ClinVar as [Benign]. Clinvar id is 790318.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SNX9NM_016224.5 linkuse as main transcriptc.538G>A p.Asp180Asn missense_variant 6/18 ENST00000392185.8 NP_057308.1
SNX9XM_011535886.4 linkuse as main transcriptc.256G>A p.Asp86Asn missense_variant 3/15 XP_011534188.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SNX9ENST00000392185.8 linkuse as main transcriptc.538G>A p.Asp180Asn missense_variant 6/181 NM_016224.5 ENSP00000376024 P1

Frequencies

GnomAD3 genomes
AF:
0.00746
AC:
1131
AN:
151580
Hom.:
7
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00374
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.00565
Gnomad ASJ
AF:
0.00288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00708
Gnomad FIN
AF:
0.00527
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0113
Gnomad OTH
AF:
0.00962
GnomAD3 exomes
AF:
0.00830
AC:
2085
AN:
251310
Hom.:
19
AF XY:
0.00896
AC XY:
1217
AN XY:
135850
show subpopulations
Gnomad AFR exome
AF:
0.00370
Gnomad AMR exome
AF:
0.00544
Gnomad ASJ exome
AF:
0.00199
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00928
Gnomad FIN exome
AF:
0.00568
Gnomad NFE exome
AF:
0.0118
Gnomad OTH exome
AF:
0.0117
GnomAD4 exome
AF:
0.0112
AC:
16343
AN:
1461770
Hom.:
127
Cov.:
34
AF XY:
0.0112
AC XY:
8129
AN XY:
727206
show subpopulations
Gnomad4 AFR exome
AF:
0.00487
Gnomad4 AMR exome
AF:
0.00628
Gnomad4 ASJ exome
AF:
0.00237
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00860
Gnomad4 FIN exome
AF:
0.00537
Gnomad4 NFE exome
AF:
0.0127
Gnomad4 OTH exome
AF:
0.00916
GnomAD4 genome
AF:
0.00745
AC:
1130
AN:
151690
Hom.:
7
Cov.:
31
AF XY:
0.00726
AC XY:
538
AN XY:
74118
show subpopulations
Gnomad4 AFR
AF:
0.00373
Gnomad4 AMR
AF:
0.00565
Gnomad4 ASJ
AF:
0.00288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00688
Gnomad4 FIN
AF:
0.00527
Gnomad4 NFE
AF:
0.0113
Gnomad4 OTH
AF:
0.00952
Alfa
AF:
0.00937
Hom.:
11
Bravo
AF:
0.00699
TwinsUK
AF:
0.0140
AC:
52
ALSPAC
AF:
0.0156
AC:
60
ESP6500AA
AF:
0.00272
AC:
12
ESP6500EA
AF:
0.0108
AC:
93
ExAC
AF:
0.00872
AC:
1059
Asia WGS
AF:
0.00289
AC:
10
AN:
3478
EpiCase
AF:
0.0123
EpiControl
AF:
0.0122

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 16, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.58
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Benign
0.066
T
Eigen
Benign
-0.20
Eigen_PC
Benign
0.00080
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.85
D
MetaRNN
Benign
0.0042
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.0
L
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
0.33
N
REVEL
Benign
0.13
Sift
Benign
0.13
T
Sift4G
Benign
0.39
T
Polyphen
0.0020
B
Vest4
0.24
MVP
0.58
MPC
0.10
ClinPred
0.019
T
GERP RS
5.4
Varity_R
0.15
gMVP
0.24

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: rs61748681; hg19: chr6-158322995; COSMIC: COSV99060917; API