rs2691561

chr7-17908967-T-Achr7-17908967-T-C

Variant summary

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

The NM_015132.5(SNX13):c.13-11521A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,750 control chromosomes in the GnomAD database, including 15,211 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 (15211 hom., cov: 31)
• Consequence: SNX13 NM_015132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX13	NM_015132.5	c.13-11521A>T		intron_variant		ENST00000428135.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX13	ENST00000428135.7	c.13-11521A>T		intron_variant		1	NM_015132.5	P1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66908 AN: 151632 Hom.: 15197 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.441 AC: 66971 AN: 151750 Hom.: 15211 Cov.: 31 AF XY: 0.445 AC XY: 32989 AN XY: 74160

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.437

Alfa AF: 0.416 Hom.: 1663

Bravo AF: 0.446

Asia WGS AF: 0.649 AC: 2257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.9
Dann	Benign	0.84

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: rs2691561; hg19: chr7-17948590;