dbSNP rs1528533: SNX17:c.256+149G>C (chr2-27372889-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014748.4(SNX17):c.256+149G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 1,242,830 control chromosomes in the GnomAD database, including 105,222 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.46 ( 17305 hom., cov: 33)

Exomes 𝑓: 0.39 ( 87917 hom. )

Consequence

SNX17
NM_014748.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0800

Publications

17 publications found

Variant links:

Genes affected

SNX17 (HGNC:14979): (sorting nexin 17) 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, but contains a B41 domain. This protein interacts with the cytoplasmic domain of P-selectin, and may function in the intracellular trafficking of P-selectin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2012]

SNX17 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX17	NM_014748.4 link	c.256+149G>C		intron_variant	Intron 3 of 14	ENST00000233575.7	NP_055563.1	Q15036-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX17	ENST00000233575.7 link	c.256+149G>C		intron_variant	Intron 3 of 14	1	NM_014748.4	ENSP00000233575.2		Q15036-1

Frequencies

GnomAD3 genomes

AF:

0.458

AC:

69594

AN:

151992

Hom.:

17261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.645

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.469

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.429

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.383

Gnomad OTH

AF:

0.404

GnomAD4 exome

AF:

0.392

AC:

427868

AN:

1090720

Hom.:

87917

Cov.:

AF XY:

0.391

AC XY:

214893

AN XY:

549606

show subpopulations

African (AFR)

AF:

0.653

AC:

16739

AN:

25624

American (AMR)

AF:

0.544

AC:

18831

AN:

34618

Ashkenazi Jewish (ASJ)

AF:

0.339

AC:

7563

AN:

22300

East Asian (EAS)

AF:

0.131

AC:

4504

AN:

34306

South Asian (SAS)

AF:

0.418

AC:

29677

AN:

71058

European-Finnish (FIN)

AF:

0.432

AC:

19856

AN:

45920

Middle Eastern (MID)

AF:

0.342

AC:

1608

AN:

4700

European-Non Finnish (NFE)

AF:

0.386

AC:

310569

AN:

804502

Other (OTH)

AF:

0.388

AC:

18521

AN:

47692

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

12912

25823

38735

51646

64558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8942

17884

26826

35768

44710

<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:

0.458

AC:

69699

AN:

152110

Hom.:

17305

Cov.:

AF XY:

0.457

AC XY:

33985

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.645

AC:

26785

AN:

41502

American (AMR)

AF:

0.470

AC:

7184

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

1158

AN:

3468

East Asian (EAS)

AF:

0.154

AC:

797

AN:

5186

South Asian (SAS)

AF:

0.426

AC:

2054

AN:

4822

European-Finnish (FIN)

AF:

0.429

AC:

4531

AN:

10550

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.383

AC:

26016

AN:

67974

Other (OTH)

AF:

0.408

AC:

864

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1842

3684

5525

7367

9209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

616

1232

1848

2464

3080

<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:

0.428

Hom.:

1953

Bravo

AF:

0.469

Asia WGS

AF:

0.358

AC:

1245

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.60

(source)

DANN

Benign

0.41

PhyloP100

-0.080

Mutation Taster

=100/0

polymorphism (auto)

(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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over