rs12443880

chr16-50670764-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000423026.6(SNX20):c.283-2723A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0831 in 152,272 control chromosomes in the GnomAD database, including 1,399 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 0.083 (1398 hom., cov: 32)
  • Exomes 𝑓: 0.059 (1 hom.)
• Consequence: SNX20 ENST00000423026.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927272	NR_110908.1	n.388T>G		non_coding_transcript_exon_variant	2/3
SNX20	NM_001144972.2	c.283-2723A>C		intron_variant
SNX20	NM_153337.3	c.283-1616A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000570241.3	n.4340T>G		non_coding_transcript_exon_variant	2/3	1

Frequencies

GnomAD3 genomes AF: 0.0827 AC: 12585 AN: 152086 Hom.: 1385 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00501

Gnomad OTH AF: 0.0559

GnomAD4 exome AF: 0.0588 AC: 4 AN: 68 Hom.: 1 Cov.: 0 AF XY: 0.0652 AC XY: 3 AN XY: 46

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0217

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.0831 AC: 12651 AN: 152204 Hom.: 1398 Cov.: 32 AF XY: 0.0821 AC XY: 6112 AN XY: 74426

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.0621

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.00501

Gnomad4 OTH AF: 0.0563

Alfa AF: 0.0212 Hom.: 259

Bravo AF: 0.0942

Asia WGS AF: 0.0740 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.0
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12443880; hg19: chr16-50704675;