16-50671836-T-G

Variant names:

• chr16-50671836-T-G
• rs10193
• NM_182854.4:c.*1570A>C

Variant summary

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

The NM_182854.4(SNX20):​c.*1570A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,200 control chromosomes in the GnomAD database, including 6,275 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 0.17 (6275 hom., cov: 33)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: SNX20 NM_182854.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665
• Publications: 6 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]

ENSG00000260249 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182854.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX20	NM_182854.4	MANE Select	c.*1570A>C		3_prime_UTR	Exon 4 of 4	NP_878274.1
	SNX20	NM_153337.3		c.283-2688A>C		intron	N/A	NP_699168.1
	SNX20	NM_001144972.2		c.283-3795A>C		intron	N/A	NP_001138444.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX20	ENST00000330943.9	TSL:1 MANE Select	c.*1570A>C		3_prime_UTR	Exon 4 of 4	ENSP00000332062.4
	SNX20	ENST00000423026.6	TSL:1	c.283-3795A>C		intron	N/A	ENSP00000388875.2
	SNX20	ENST00000568993.5	TSL:1	n.283-2688A>C		intron	N/A	ENSP00000454863.1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25101 AN: 152072 Hom.: 6236 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.0105

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.00566

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.166 AC: 25197 AN: 152190 Hom.: 6275 Cov.: 33 AF XY: 0.161 AC XY: 11979 AN XY: 74408

African (AFR) AF: 0.541 AC: 22402 AN: 41444

American (AMR) AF: 0.0904 AC: 1384 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3472

East Asian (EAS) AF: 0.106 AC: 550 AN: 5166

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4824

European-Finnish (FIN) AF: 0.0105 AC: 112 AN: 10624

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.00566 AC: 385 AN: 68032

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.0621 Hom.: 2452

Bravo AF: 0.188

Asia WGS AF: 0.0940 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.7
DANN	Benign	0.68
PhyloP100		0.67
Mutation Taster		=100/0	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: rs10193; hg19: chr16-50705747;