Genetic Variant SNX7:p.Pro11Ser (chr1-98661762-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_015976.5(SNX7):c.31C>T(p.Pro11Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P11L) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SNX7
NM_015976.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.30

Publications

0 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]

SNX7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.06896111).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015976.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SNX7	NM_015976.5	MANE Select	c.31C>T	p.Pro11Ser	missense	Exon 1 of 9	NP_057060.2	Q9UNH6-3
SNX7	NM_152238.4		c.31C>T	p.Pro11Ser	missense	Exon 1 of 8	NP_689424.2	E9PNL2
SNX7	NM_001364903.1		c.-282C>T		5_prime_UTR	Exon 1 of 10	NP_001351832.1	Q9UNH6-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SNX7	ENST00000306121.8	TSL:1 MANE Select	c.31C>T	p.Pro11Ser	missense	Exon 1 of 9	ENSP00000304429.3	Q9UNH6-3
SNX7	ENST00000971618.1		c.31C>T	p.Pro11Ser	missense	Exon 1 of 9	ENSP00000641677.1
SNX7	ENST00000851356.1		c.31C>T	p.Pro11Ser	missense	Exon 1 of 9	ENSP00000521415.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1087648

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

513600

African (AFR)

AF:

0.00

AC:

AN:

22758

American (AMR)

AF:

0.00

AC:

AN:

8286

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14188

East Asian (EAS)

AF:

0.00

AC:

AN:

26364

South Asian (SAS)

AF:

0.00

AC:

AN:

19468

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32606

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2906

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

917636

Other (OTH)

AF:

0.00

AC:

AN:

43436

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.75

CADD

Benign

(source)

DANN

Benign

0.79

DEOGEN2

Benign

0.0046

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.18

LIST_S2

Benign

0.68

M_CAP

Benign

0.0085

MetaRNN

Benign

0.069

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.0

PhyloP100

1.3

PrimateAI

Pathogenic

0.85

PROVEAN

Benign

-0.17

REVEL

Benign

0.027

Sift

Benign

0.18

Sift4G

Benign

0.45

Polyphen

0.0010

Vest4

0.098

MutPred

0.17

Gain of phosphorylation at P11 (P = 0.0082)

MVP

0.15

MPC

0.092

ClinPred

0.075

GERP RS

1.1

PromoterAI

-0.041

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

gMVP

0.23

Mutation Taster

=99/1

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over