rs8059649

Variant names:

• chr16-50670251-T-C
• rs8059649
• ENST00000423026.6:c.283-2210A>G

Variant summary

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

The ENST00000423026.6(SNX20):​c.283-2210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 152,438 control chromosomes in the GnomAD database, including 321 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 0.041 (321 hom., cov: 32)
  • Exomes 𝑓: 0.0050 (0 hom.)
• Consequence: SNX20 ENST00000423026.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 4 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX20	NM_153337.3	c.283-1103A>G		intron_variant	Intron 3 of 3		NP_699168.1
SNX20	NM_001144972.2	c.283-2210A>G		intron_variant	Intron 3 of 3		NP_001138444.1
LOC101927272	NR_110908.1	n.307-432T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX20	ENST00000423026.6	c.283-2210A>G		intron_variant	Intron 3 of 3	1		ENSP00000388875.2
SNX20	ENST00000568993.5	n.283-1103A>G		intron_variant	Intron 3 of 4	1		ENSP00000454863.1
ENSG00000260249	ENST00000570241.3	n.4259-432T>C		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6177 AN: 152118 Hom.: 322 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.00766

Gnomad FIN AF: 0.00782

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.0368

GnomAD4 exome AF: 0.00495 AC: 1 AN: 202 Hom.: 0 Cov.: 0 AF XY: 0.00610 AC XY: 1 AN XY: 164

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00602 AC: 1 AN: 166

Other (OTH) AF: 0.00 AC: 0 AN: 18

GnomAD4 genome AF: 0.0407 AC: 6190 AN: 152236 Hom.: 321 Cov.: 32 AF XY: 0.0397 AC XY: 2956 AN XY: 74440

African (AFR) AF: 0.114 AC: 4724 AN: 41532

American (AMR) AF: 0.0310 AC: 474 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.139 AC: 717 AN: 5168

South Asian (SAS) AF: 0.00746 AC: 36 AN: 4826

European-Finnish (FIN) AF: 0.00782 AC: 83 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00113 AC: 77 AN: 68002

Other (OTH) AF: 0.0364 AC: 77 AN: 2114

Alfa AF: 0.0302 Hom.: 28

Bravo AF: 0.0481

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.35
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8059649; hg19: chr16-50704162;