rs1568818

Positions:

• chr7-17897956-A-G
• chr7-17897956-A-T

Variant summary

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

The NM_015132.5(SNX13):​c.13-510T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,538 control chromosomes in the GnomAD database, including 15,330 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 0.44 (15330 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: SNX13 NM_015132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

SNX13 (HGNC:21335): (sorting nexin 13) This gene encodes a PHOX domain- and RGS domain-containing protein that belongs to the sorting nexin (SNX) family and the regulator of G protein signaling (RGS) family. The PHOX domain is a phosphoinositide binding domain, and the SNX family members are involved in intracellular trafficking. The RGS family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. The RGS domain of this protein interacts with G alpha(s), accelerates its GTP hydrolysis, and attenuates G alpha(s)-mediated signaling. Overexpression of this protein delayes lysosomal degradation of the epidermal growth factor receptor. Because of its bifunctional role, this protein may link heterotrimeric G protein signaling and vesicular trafficking. [provided by RefSeq, Jul 2008]

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 (SAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX13	NM_015132.5	c.13-510T>C		intron_variant		ENST00000428135.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX13	ENST00000428135.7	c.13-510T>C		intron_variant		1	NM_015132.5	P1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67212 AN: 151418 Hom.: 15320 Cov.: 30

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.444 AC: 67270 AN: 151538 Hom.: 15330 Cov.: 30 AF XY: 0.448 AC XY: 33148 AN XY: 74040

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.440

Alfa AF: 0.419 Hom.: 1676

Bravo AF: 0.452

Asia WGS AF: 0.645 AC: 2227 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.30

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: rs1568818; hg19: chr7-17937579;