16-50681068-T-C

Variant names:

• chr16-50681068-T-C
• rs2287195
• NM_182854.4:c.-10+122A>G

Variant summary

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

The NM_182854.4(SNX20):​c.-10+122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,290 control chromosomes in the GnomAD database, including 40,920 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 0.72 (40872 hom., cov: 32)
  • Exomes 𝑓: 0.73 (48 hom.)
• Consequence: SNX20 NM_182854.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 18 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 (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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.-10+122A>G		intron	N/A	NP_878274.1
	SNX20	NM_153337.3		c.-10+122A>G		intron	N/A	NP_699168.1
	SNX20	NM_001144972.2		c.-10+122A>G		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.-10+122A>G		intron	N/A	ENSP00000332062.4
	SNX20	ENST00000423026.6	TSL:1	c.-10+122A>G		intron	N/A	ENSP00000388875.2
	SNX20	ENST00000568993.5	TSL:1	n.-10+122A>G		intron	N/A	ENSP00000454863.1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109554 AN: 151990 Hom.: 40832 Cov.: 32

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.701

GnomAD4 exome AF: 0.731 AC: 133 AN: 182 Hom.: 48 AF XY: 0.700 AC XY: 84 AN XY: 120

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.500 AC: 3 AN: 6

South Asian (SAS) AF: 0.750 AC: 6 AN: 8

European-Finnish (FIN) AF: 1.00 AC: 6 AN: 6

Middle Eastern (MID) AF: 0.500 AC: 2 AN: 4

European-Non Finnish (NFE) AF: 0.728 AC: 99 AN: 136

Other (OTH) AF: 0.688 AC: 11 AN: 16

GnomAD4 genome AF: 0.721 AC: 109648 AN: 152108 Hom.: 40872 Cov.: 32 AF XY: 0.711 AC XY: 52832 AN XY: 74358

African (AFR) AF: 0.821 AC: 34049 AN: 41484

American (AMR) AF: 0.633 AC: 9674 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2865 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1316 AN: 5160

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4820

European-Finnish (FIN) AF: 0.703 AC: 7447 AN: 10590

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50083 AN: 67972

Other (OTH) AF: 0.696 AC: 1471 AN: 2112

Alfa AF: 0.718 Hom.: 9178

Bravo AF: 0.721

Asia WGS AF: 0.342 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.40
PhyloP100		-1.3
PromoterAI		0.055	Neutral
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: rs2287195; hg19: chr16-50714979;