rs12448797

Variant names:

• chr16-50669663-T-C
• rs12448797
• ENST00000423026.6:c.283-1622A>G

Variant summary

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

The ENST00000423026.6(SNX20):​c.283-1622A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,384 control chromosomes in the GnomAD database, including 3,731 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 0.13 (3731 hom., cov: 32)
  • Exomes 𝑓: 0.0027 (0 hom.)
• Consequence: SNX20 ENST00000423026.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.630
• Publications: 7 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX20	NM_153337.3	c.283-515A>G		intron_variant	Intron 3 of 3		NP_699168.1
SNX20	NM_001144972.2	c.283-1622A>G		intron_variant	Intron 3 of 3		NP_001138444.1
LOC101927272	NR_110908.1	n.306+503T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX20	ENST00000423026.6	c.283-1622A>G		intron_variant	Intron 3 of 3	1		ENSP00000388875.2
SNX20	ENST00000568993.5	n.283-515A>G		intron_variant	Intron 3 of 4	1		ENSP00000454863.1
ENSG00000260249	ENST00000570241.3	n.4258+503T>C		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20451 AN: 151892 Hom.: 3709 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.0175

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00606

Gnomad OTH AF: 0.0990

GnomAD4 exome AF: 0.00267 AC: 1 AN: 374 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 214

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 44

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10

East Asian (EAS) AF: 0.0714 AC: 1 AN: 14

South Asian (SAS) AF: 0.00 AC: 0 AN: 24

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 244

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

GnomAD4 genome AF: 0.135 AC: 20518 AN: 152010 Hom.: 3731 Cov.: 32 AF XY: 0.132 AC XY: 9781 AN XY: 74312

African (AFR) AF: 0.408 AC: 16912 AN: 41402

American (AMR) AF: 0.0931 AC: 1423 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1255 AN: 5164

South Asian (SAS) AF: 0.0150 AC: 72 AN: 4808

European-Finnish (FIN) AF: 0.0175 AC: 185 AN: 10598

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00606 AC: 412 AN: 67966

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.0932 Hom.: 424

Bravo AF: 0.155

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.2
DANN	Benign	0.48
PhyloP100		0.63
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: rs12448797; hg19: chr16-50703574;