rs1131716

Variant names:

• chr16-50677423-G-A
• rs1131716
• NM_182854.4:c.104C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-50677423-G-A
• chr16-50677423-G-C
• chr16-50677423-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (3230 hom., cov: 32)
  • Exomes 𝑓: 0.020 (3239 hom.)
• Consequence: SNX20 NM_182854.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 16 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4	ENST00000330943.9	NP_878274.1
SNX20	NM_153337.3	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4		NP_699168.1
SNX20	NM_001144972.2	c.104C>T	p.Pro35Leu	missense_variant	Exon 2 of 4		NP_001138444.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18405 AN: 152096 Hom.: 3218 Cov.: 32

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

GnomAD2 exomes AF: 0.0437 AC: 10685 AN: 244488 AF XY: 0.0348

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 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.: 31 AF XY: 0.0182 AC XY: 13157 AN XY: 723202

African (AFR) AF: 0.401 AC: 13225 AN: 32950

American (AMR) AF: 0.0406 AC: 1776 AN: 43790

Ashkenazi Jewish (ASJ) AF: 0.0120 AC: 311 AN: 25904

East Asian (EAS) AF: 0.133 AC: 5213 AN: 39108

South Asian (SAS) AF: 0.00950 AC: 809 AN: 85148

European-Finnish (FIN) AF: 0.0103 AC: 548 AN: 53186

Middle Eastern (MID) AF: 0.0435 AC: 249 AN: 5728

European-Non Finnish (NFE) AF: 0.00370 AC: 4098 AN: 1108296

Other (OTH) AF: 0.0380 AC: 2278 AN: 59996

GnomAD4 genome AF: 0.121 AC: 18455 AN: 152214 Hom.: 3230 Cov.: 32 AF XY: 0.119 AC XY: 8888 AN XY: 74428

African (AFR) AF: 0.387 AC: 16055 AN: 41492

American (AMR) AF: 0.0718 AC: 1098 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.107 AC: 552 AN: 5182

South Asian (SAS) AF: 0.0130 AC: 63 AN: 4828

European-Finnish (FIN) AF: 0.0106 AC: 112 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00518 AC: 352 AN: 68012

Other (OTH) AF: 0.0786 AC: 166 AN: 2112

Alfa AF: 0.0468 Hom.: 3268

Bravo AF: 0.137

TwinsUK AF: 0.00270 AC: 10

ALSPAC AF: 0.00363 AC: 14

ESP6500AA AF: 0.374 AC: 1646

ESP6500EA AF: 0.00360 AC: 31

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	T
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	N
LIST_S2	Benign	0.60	T;.;T;T
MetaRNN	Benign	0.00063	T;T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Uncertain	2.3	M;M;M;.
PhyloP100		-0.035
PrimateAI	Benign	0.30	T
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	T
GERP RS		-0.37
Varity_R		0.027
gMVP		0.30
Mutation Taster		=99/1	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

Other links and lift over

dbSNP: rs1131716; hg19: chr16-50711334; COSMIC: COSV56056475;