rs6596

Variant names:

• chr16-50675812-G-A
• rs6596
• NM_182854.4:c.240C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-50675812-G-A
• chr16-50675812-G-C
• chr16-50675812-G-T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_182854.4(SNX20):​c.240C>T​(p.Ile80Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 1,613,286 control chromosomes in the GnomAD database, including 19,752 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 0.11 (1241 hom., cov: 32)
  • Exomes 𝑓: 0.15 (18511 hom.)
• Consequence: SNX20 NM_182854.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 20 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BP7: Synonymous conserved (PhyloP=-0.028 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX20	NM_182854.4	c.240C>T	p.Ile80Ile	synonymous_variant	Exon 3 of 4	ENST00000330943.9	NP_878274.1
SNX20	NM_153337.3	c.240C>T	p.Ile80Ile	synonymous_variant	Exon 3 of 4		NP_699168.1
SNX20	NM_001144972.2	c.240C>T	p.Ile80Ile	synonymous_variant	Exon 3 of 4		NP_001138444.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX20	ENST00000330943.9	c.240C>T	p.Ile80Ile	synonymous_variant	Exon 3 of 4	1	NM_182854.4	ENSP00000332062.4
SNX20	ENST00000423026.6	c.240C>T	p.Ile80Ile	synonymous_variant	Exon 3 of 4	1		ENSP00000388875.2
SNX20	ENST00000568993.5	n.240C>T		non_coding_transcript_exon_variant	Exon 3 of 5	1		ENSP00000454863.1
SNX20	ENST00000300590.7	c.240C>T	p.Ile80Ile	synonymous_variant	Exon 3 of 4	2		ENSP00000300590.3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16367 AN: 152110 Hom.: 1242 Cov.: 32

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0577

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.140

GnomAD2 exomes AF: 0.106 AC: 26480 AN: 250486 AF XY: 0.108

Gnomad AFR exome AF: 0.0261

Gnomad AMR exome AF: 0.0776

Gnomad ASJ exome AF: 0.146

Gnomad EAS exome AF: 0.000219

Gnomad FIN exome AF: 0.0613

Gnomad NFE exome AF: 0.167

Gnomad OTH exome AF: 0.124

GnomAD4 exome AF: 0.147 AC: 215491 AN: 1461058 Hom.: 18511 Cov.: 32 AF XY: 0.145 AC XY: 105129 AN XY: 726852

African (AFR) AF: 0.0250 AC: 837 AN: 33420

American (AMR) AF: 0.0809 AC: 3604 AN: 44536

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 3818 AN: 26112

East Asian (EAS) AF: 0.000303 AC: 12 AN: 39654

South Asian (SAS) AF: 0.0304 AC: 2618 AN: 86162

European-Finnish (FIN) AF: 0.0627 AC: 3347 AN: 53402

Middle Eastern (MID) AF: 0.121 AC: 696 AN: 5762

European-Non Finnish (NFE) AF: 0.173 AC: 192796 AN: 1111636

Other (OTH) AF: 0.129 AC: 7763 AN: 60374

GnomAD4 genome AF: 0.107 AC: 16364 AN: 152228 Hom.: 1241 Cov.: 32 AF XY: 0.102 AC XY: 7581 AN XY: 74432

African (AFR) AF: 0.0304 AC: 1264 AN: 41556

American (AMR) AF: 0.118 AC: 1798 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4830

European-Finnish (FIN) AF: 0.0577 AC: 611 AN: 10598

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11546 AN: 67990

Other (OTH) AF: 0.139 AC: 293 AN: 2110

Alfa AF: 0.150 Hom.: 5746

Bravo AF: 0.110

Asia WGS AF: 0.0160 AC: 57 AN: 3478

EpiCase AF: 0.178

EpiControl AF: 0.171

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	5.8
DANN	Benign	0.84
PhyloP100		-0.028
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: rs6596; hg19: chr16-50709723; COSMIC: COSV56059296; COSMIC: COSV56059296;