Variant 1-98695628-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015976.5(SNX7):c.750C>A(p.Phe250Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00603 in 1,613,282 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0045 ( 7 hom., cov: 32)

Exomes 𝑓: 0.0062 ( 51 hom. )

Consequence

SNX7
NM_015976.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.13

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.011921674).

BP6

Variant 1-98695628-C-A is Benign according to our data. Variant chr1-98695628-C-A is described in ClinVar as [Benign]. Clinvar id is 719339.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX7	NM_015976.5 linkuse as main transcript	c.750C>A	p.Phe250Leu	missense_variant	5/9	ENST00000306121.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX7	ENST00000306121.8 linkuse as main transcript	c.750C>A	p.Phe250Leu	missense_variant	5/9	1	NM_015976.5	P1	Q9UNH6-3
SNX7	ENST00000528824.1 linkuse as main transcript	c.*570C>A		3_prime_UTR_variant, NMD_transcript_variant	6/9	1
SNX7	ENST00000529992.5 linkuse as main transcript	c.585C>A	p.Phe195Leu	missense_variant	4/8	2

Frequencies

GnomAD3 genomes

AF:

0.00455

AC:

692

AN:

152014

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00109

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00151

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00187

Gnomad FIN

AF:

0.0158

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00648

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00481

AC:

1210

AN:

251364

Hom.:

AF XY:

0.00504

AC XY:

685

AN XY:

135896

show subpopulations

Gnomad AFR exome

AF:

0.000801

Gnomad AMR exome

AF:

0.00165

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00415

Gnomad FIN exome

AF:

0.0131

Gnomad NFE exome

AF:

0.00620

Gnomad OTH exome

AF:

0.00359

GnomAD4 exome

AF:

0.00619

AC:

9041

AN:

1461148

Hom.:

Cov.:

AF XY:

0.00605

AC XY:

4398

AN XY:

726936

show subpopulations

Gnomad4 AFR exome

AF:

0.000896

Gnomad4 AMR exome

AF:

0.00174

Gnomad4 ASJ exome

AF:

0.000230

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00399

Gnomad4 FIN exome

AF:

0.0127

Gnomad4 NFE exome

AF:

0.00673

Gnomad4 OTH exome

AF:

0.00691

GnomAD4 genome

AF:

0.00454

AC:

691

AN:

152134

Hom.:

Cov.:

AF XY:

0.00510

AC XY:

379

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.00108

Gnomad4 AMR

AF:

0.00150

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.0158

Gnomad4 NFE

AF:

0.00647

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00506

Hom.:

Bravo

AF:

0.00365

TwinsUK

AF:

0.00728

AC:

ALSPAC

AF:

0.00571

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00605

AC:

ExAC

AF:

0.00442

AC:

537

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00556

EpiControl

AF:

0.00640

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 submitter

clinical testing

Invitae

Mar 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Uncertain

0.070

Cadd

Uncertain

Dann

Uncertain

1.0

DEOGEN2

Benign

0.19

T;.

Eigen

Pathogenic

0.69

Eigen_PC

Pathogenic

0.67

FATHMM_MKL

Uncertain

0.94

LIST_S2

Uncertain

0.92

D;D

MetaRNN

Benign

0.012

T;T

MetaSVM

Benign

-0.91

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.68

PROVEAN

Pathogenic

-5.1

D;D

REVEL

Uncertain

0.30

Sift

Benign

0.056

T;T

Sift4G

Uncertain

0.013

D;D

Polyphen

1.0

D;D

Vest4

0.94

MutPred

0.56

Gain of MoRF binding (P = 0.1485);.;

MVP

0.72

MPC

0.52

ClinPred

0.034

GERP RS

5.7

gMVP

0.75

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