dbSNP rs4665972: SNX17:c.774+77T>C (chr2-27375230-T-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.774+77T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 1,324,074 control chromosomes in the GnomAD database, including 261,075 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 0.68 ( 37070 hom., cov: 30)

Exomes 𝑓: 0.61 ( 224005 hom. )

Consequence

SNX17
NM_014748.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.29

Publications

70 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:

Genome browser will be placed here

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.903 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	UniProt
SNX17	NM_014748.4	MANE Select	c.774+77T>C	intron	N/A	NP_055563.1	Q15036-1
SNX17	NM_001267059.2		c.738+77T>C	intron	N/A	NP_001253988.1	B4DTB8
SNX17	NM_001267061.2		c.714+77T>C	intron	N/A	NP_001253990.1	B4DQ37

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SNX17	ENST00000233575.7	TSL:1 MANE Select	c.774+77T>C	intron	N/A	ENSP00000233575.2	Q15036-1
SNX17	ENST00000440760.5	TSL:1	n.*619+77T>C	intron	N/A	ENSP00000399727.1	F8WFA0
SNX17	ENST00000453453.1	TSL:1	n.*301+77T>C	intron	N/A	ENSP00000401922.1	F8WEG6

Frequencies

GnomAD3 genomes

AF:

0.682

AC:

103458

AN:

151754

Hom.:

36997

Cov.:

show subpopulations

Gnomad AFR

AF:

0.911

Gnomad AMI

AF:

0.666

Gnomad AMR

AF:

0.628

Gnomad ASJ

AF:

0.454

Gnomad EAS

AF:

0.492

Gnomad SAS

AF:

0.749

Gnomad FIN

AF:

0.611

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.590

Gnomad OTH

AF:

0.618

GnomAD4 exome

AF:

0.612

AC:

717100

AN:

1172202

Hom.:

224005

AF XY:

0.614

AC XY:

361771

AN XY:

589544

show subpopulations

African (AFR)

AF:

0.919

AC:

25513

AN:

27748

American (AMR)

AF:

0.673

AC:

25905

AN:

38500

Ashkenazi Jewish (ASJ)

AF:

0.462

AC:

10834

AN:

23460

East Asian (EAS)

AF:

0.460

AC:

16890

AN:

36688

South Asian (SAS)

AF:

0.744

AC:

57861

AN:

77822

European-Finnish (FIN)

AF:

0.621

AC:

28257

AN:

45516

Middle Eastern (MID)

AF:

0.524

AC:

2506

AN:

4780

European-Non Finnish (NFE)

AF:

0.598

AC:

518336

AN:

866958

Other (OTH)

AF:

0.611

AC:

30998

AN:

50730

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

13740

27481

41221

54962

68702

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13198

26396

39594

52792

65990

<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:

0.682

AC:

103603

AN:

151872

Hom.:

37070

Cov.:

AF XY:

0.680

AC XY:

50448

AN XY:

74210

show subpopulations

African (AFR)

AF:

0.911

AC:

37786

AN:

41474

American (AMR)

AF:

0.628

AC:

9582

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.454

AC:

1572

AN:

3466

East Asian (EAS)

AF:

0.492

AC:

2526

AN:

5132

South Asian (SAS)

AF:

0.750

AC:

3614

AN:

4820

European-Finnish (FIN)

AF:

0.611

AC:

6430

AN:

10524

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.590

AC:

40032

AN:

67898

Other (OTH)

AF:

0.622

AC:

1309

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1519

3038

4556

6075

7594

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

796

1592

2388

3184

3980

<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:

0.925

Hom.:

39091

Bravo

AF:

0.691

Asia WGS

AF:

0.677

AC:

2350

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.73

(source)

DANN

Benign

0.15

PhyloP100

-3.3

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

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over