Genetic Variant SNX8:c.1284+16T>C (chr7-2256858-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_013321.4(SNX8):c.1284+16T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 1,604,230 control chromosomes in the GnomAD database, including 703,111 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.88 ( 59570 hom., cov: 35)

Exomes 𝑓: 0.94 ( 643541 hom. )

Consequence

SNX8
NM_013321.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.786

Variant links:

Genes affected

SNX8 (HGNC:14972): (sorting nexin 8) Enables identical protein binding activity and phosphatidylinositol binding activity. Involved in early endosome to Golgi transport and intracellular protein transport. Located in early endosome membrane. Colocalizes with retromer complex. [provided by Alliance of Genome Resources, Apr 2022]

SNX8 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 7-2256858-A-G is Benign according to our data. Variant chr7-2256858-A-G is described in ClinVar as [Benign]. Clinvar id is 1291057.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX8	NM_013321.4 link	c.1284+16T>C		intron_variant	Intron 10 of 10	ENST00000222990.8	NP_037453.1	Q9Y5X2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX8	ENST00000222990.8 link	c.1284+16T>C		intron_variant	Intron 10 of 10	1	NM_013321.4	ENSP00000222990.3		Q9Y5X2
SNX8	ENST00000480807.1 link	n.404+16T>C		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.879

AC:

133694

AN:

152114

Hom.:

59525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.733

Gnomad AMI

AF:

0.966

Gnomad AMR

AF:

0.892

Gnomad ASJ

AF:

0.886

Gnomad EAS

AF:

0.813

Gnomad SAS

AF:

0.868

Gnomad FIN

AF:

0.954

Gnomad MID

AF:

0.918

Gnomad NFE

AF:

0.956

Gnomad OTH

AF:

0.897

GnomAD2 exomes

AF:

0.905

AC:

220840

AN:

244002

AF XY:

0.910

show subpopulations

Gnomad AFR exome

AF:

0.735

Gnomad AMR exome

AF:

0.872

Gnomad ASJ exome

AF:

0.886

Gnomad EAS exome

AF:

0.812

Gnomad FIN exome

AF:

0.955

Gnomad NFE exome

AF:

0.956

Gnomad OTH exome

AF:

0.928

GnomAD4 exome

AF:

0.940

AC:

1364988

AN:

1451998

Hom.:

643541

Cov.:

AF XY:

0.939

AC XY:

677135

AN XY:

721258

show subpopulations

Gnomad4 AFR exome

AF:

0.724

AC:

24058

AN:

33216

Gnomad4 AMR exome

AF:

0.873

AC:

38306

AN:

43860

Gnomad4 ASJ exome

AF:

0.888

AC:

22802

AN:

25690

Gnomad4 EAS exome

AF:

0.806

AC:

31796

AN:

39440

Gnomad4 SAS exome

AF:

0.870

AC:

74362

AN:

85486

Gnomad4 FIN exome

AF:

0.956

AC:

50196

AN:

52520

Gnomad4 NFE exome

AF:

0.961

AC:

1062885

AN:

1106388

Gnomad4 Remaining exome

AF:

0.929

AC:

55661

AN:

59922

Heterozygous variant carriers

3851

7702

11552

15403

19254

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

21580

43160

64740

86320

107900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.879

AC:

133790

AN:

152232

Hom.:

59570

Cov.:

AF XY:

0.878

AC XY:

65380

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.733

AC:

0.732916

AN:

0.732916

Gnomad4 AMR

AF:

0.892

AC:

0.892381

AN:

0.892381

Gnomad4 ASJ

AF:

0.886

AC:

0.885945

AN:

0.885945

Gnomad4 EAS

AF:

0.814

AC:

0.814026

AN:

0.814026

Gnomad4 SAS

AF:

0.869

AC:

0.868574

AN:

0.868574

Gnomad4 FIN

AF:

0.954

AC:

0.953578

AN:

0.953578

Gnomad4 NFE

AF:

0.956

AC:

0.956489

AN:

0.956489

Gnomad4 OTH

AF:

0.898

AC:

0.898393

AN:

0.898393

Heterozygous variant carriers

771

1542

2312

3083

3854

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

890

1780

2670

3560

4450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.916

Hom.:

22239

Bravo

AF:

0.869

Asia WGS

AF:

0.876

AC:

3040

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Apr 14, 2019

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.3

DANN

Benign

0.17

Mutation Taster

=100/0

polymorphism (auto)

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