Variant rs1131716 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_182854.4(SNX20):c.104C>T(p.Pro35Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0292 in 1,606,320 control chromosomes in the GnomAD database, including 6,469 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.12 ( 3230 hom., cov: 32)

Exomes 𝑓: 0.020 ( 3239 hom. )

Consequence

SNX20
NM_182854.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0350

Variant links:

Genes affected

SNX20 (HGNC:30390): (sorting nexin 20) SNX20 interacts with the cytoplasmic domain of PSGL1 (SELPLG; MIM 600738) and cycles PSGL1 into endosomes.[supplied by OMIM, Feb 2010]

SNX20 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=6.251335E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX20	NM_182854.4 link	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4	ENST00000330943.9	NP_878274.1	Q7Z614-1
SNX20	NM_153337.3 link	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4		NP_699168.1	Q7Z614-3
SNX20	NM_001144972.2 link	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4		NP_001138444.1	Q7Z614-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SNX20	ENST00000330943.9 link	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4	1	NM_182854.4	ENSP00000332062.4	Q7Z614-1
SNX20	ENST00000423026.6 link	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4	1		ENSP00000388875.2	Q7Z614-4
SNX20	ENST00000568993.5 link	n.104C>T		non_coding_transcript_exon_variant	Exon 2 of 5	1		ENSP00000454863.1	Q7Z614-3
SNX20	ENST00000300590.7 link	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4	2		ENSP00000300590.3	Q7Z614-3

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18405

AN:

152096

Hom.:

3218

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0716

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.0141

Gnomad FIN

AF:

0.0106

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.00517

Gnomad OTH

AF:

0.0789

GnomAD3 exomes

AF:

0.0437

AC:

10685

AN:

244488

Hom.:

1385

AF XY:

0.0348

AC XY:

4596

AN XY:

132250

show subpopulations

Gnomad AFR exome

AF:

0.398

Gnomad AMR exome

AF:

0.0360

Gnomad ASJ exome

AF:

0.0107

Gnomad EAS exome

AF:

0.113

Gnomad SAS exome

AF:

0.00856

Gnomad FIN exome

AF:

0.0108

Gnomad NFE exome

AF:

0.00454

Gnomad OTH exome

AF:

0.0283

GnomAD4 exome

AF:

0.0196

AC:

28507

AN:

1454106

Hom.:

3239

Cov.:

AF XY:

0.0182

AC XY:

13157

AN XY:

723202

show subpopulations

Gnomad4 AFR exome

AF:

0.401

Gnomad4 AMR exome

AF:

0.0406

Gnomad4 ASJ exome

AF:

0.0120

Gnomad4 EAS exome

AF:

0.133

Gnomad4 SAS exome

AF:

0.00950

Gnomad4 FIN exome

AF:

0.0103

Gnomad4 NFE exome

AF:

0.00370

Gnomad4 OTH exome

AF:

0.0380

GnomAD4 genome

AF:

0.121

AC:

18455

AN:

152214

Hom.:

3230

Cov.:

AF XY:

0.119

AC XY:

8888

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.387

Gnomad4 AMR

AF:

0.0718

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.107

Gnomad4 SAS

AF:

0.0130

Gnomad4 FIN

AF:

0.0106

Gnomad4 NFE

AF:

0.00518

Gnomad4 OTH

AF:

0.0786

Alfa

AF:

0.0278

Hom.:

1116

Bravo

AF:

0.137

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00363

AC:

ESP6500AA

AF:

0.374

AC:

1646

ESP6500EA

AF:

0.00360

AC:

ExAC

AF:

0.0510

AC:

6194

Asia WGS

AF:

0.0830

AC:

288

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.73

BayesDel_noAF

Benign

-0.68

CADD

Benign

2.1

DANN

Benign

0.51

DEOGEN2

Benign

0.0053

.;.;T;.

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.079

LIST_S2

Benign

0.60

T;.;T;T

MetaRNN

Benign

0.00063

T;T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Uncertain

2.3

M;M;M;.

PrimateAI

Benign

0.30

PROVEAN

Benign

-2.2

N;N;N;.

REVEL

Benign

0.028

Sift

Benign

0.50

T;T;T;.

Sift4G

Benign

0.69

T;T;T;T

Polyphen

0.023

B;B;B;.

Vest4

0.13

MPC

0.51

ClinPred

0.0060

GERP RS

-0.37

Varity_R

0.027

gMVP

0.30

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over