rs1463259

Variant names:

• chr8-81825510-T-C
• rs1463259
• NM_152836.3:c.463-1570A>G

Variant summary

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

The NM_152836.3(SNX16):​c.463-1570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,068 control chromosomes in the GnomAD database, including 46,669 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 0.78 (46669 hom., cov: 32)
• Consequence: SNX16 NM_152836.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 8 publications found

Genes affected

SNX16 (HGNC:14980): (sorting nexin 16) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. The protein encoded by this gene associates with late endosome membranes as is involved in tubule formation, cholesterol transport, and transport of tetraspanin CD81. The encoded protein also inhibits cell migration and tumorigenesis. [provided by RefSeq, Jan 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX16	NM_152836.3	c.463-1570A>G		intron_variant	Intron 3 of 7	ENST00000345957.9	NP_690049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX16	ENST00000345957.9	c.463-1570A>G		intron_variant	Intron 3 of 7	1	NM_152836.3	ENSP00000322652.4

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117961 AN: 151952 Hom.: 46606 Cov.: 32

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.762

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.776 AC: 118079 AN: 152068 Hom.: 46669 Cov.: 32 AF XY: 0.772 AC XY: 57412 AN XY: 74332

African (AFR) AF: 0.903 AC: 37477 AN: 41518

American (AMR) AF: 0.734 AC: 11207 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2412 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2036 AN: 5140

South Asian (SAS) AF: 0.797 AC: 3849 AN: 4828

European-Finnish (FIN) AF: 0.719 AC: 7575 AN: 10538

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 51001 AN: 67980

Other (OTH) AF: 0.765 AC: 1614 AN: 2110

Alfa AF: 0.758 Hom.: 38420

Bravo AF: 0.778

Asia WGS AF: 0.669 AC: 2322 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.80
PhyloP100		0.0060
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: rs1463259; hg19: chr8-82737745;