Genetic Variant 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014748.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SNX17	NM_014748.4	MANE Select	c.256+149G>C	intron	N/A	NP_055563.1
SNX17	NM_001267059.2		c.220+149G>C	intron	N/A	NP_001253988.1
SNX17	NM_001267061.2		c.196+149G>C	intron	N/A	NP_001253990.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SNX17	ENST00000233575.7	TSL:1 MANE Select	c.256+149G>C	intron	N/A	ENSP00000233575.2
SNX17	ENST00000440760.5	TSL:1	n.*102-358G>C	intron	N/A	ENSP00000399727.1
SNX17	ENST00000453453.1	TSL:1	n.64-358G>C	intron	N/A	ENSP00000401922.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over