16-50681068-T-C

Position:

• chr16-50681068-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX20	NM_182854.4	c.-10+122A>G		intron_variant		ENST00000330943.9	NP_878274.1
SNX20	NM_153337.3	c.-10+122A>G		intron_variant			NP_699168.1
SNX20	NM_001144972.2	c.-10+122A>G		intron_variant			NP_001138444.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX20	ENST00000330943.9	c.-10+122A>G		intron_variant		1	NM_182854.4	ENSP00000332062.4
SNX20	ENST00000423026.6	c.-10+122A>G		intron_variant		1		ENSP00000388875.2
SNX20	ENST00000568993.5	n.-10+122A>G		intron_variant		1		ENSP00000454863.1
SNX20	ENST00000300590.7	c.-10+122A>G		intron_variant		2		ENSP00000300590.3

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

Gnomad4 AFR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.728

Gnomad4 OTH exome AF: 0.688

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

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.696

Alfa AF: 0.711 Hom.: 7615

Bravo AF: 0.721

Asia WGS AF: 0.342 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs2287195; hg19: chr16-50714979;