rs1463259

chr8-81825510-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SNX16	NM_152836.3	c.463-1570A>G		intron_variant		ENST00000345957.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX16	ENST00000345957.9	c.463-1570A>G		intron_variant		1	NM_152836.3	P1

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

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.765

Alfa AF: 0.762 Hom.: 27676

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

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: rs1463259; hg19: chr8-82737745;