rs2691561

Variant names:

• chr7-17908967-T-A
• rs2691561
• NM_015132.5:c.13-11521A>T

Your query was ambiguous. Multiple possible variants found:

• chr7-17908967-T-A
• chr7-17908967-T-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000306369 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015132.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX13	NM_015132.5	MANE Select	c.13-11521A>T		intron	N/A	NP_055947.1	Q9Y5W8-2
	SNX13	NM_001350862.2		c.13-11521A>T		intron	N/A	NP_001337791.1	Q9Y5W8-1
	SNX13	NM_001350863.2		c.-221-11521A>T		intron	N/A	NP_001337792.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX13	ENST00000428135.7	TSL:1 MANE Select	c.13-11521A>T		intron	N/A	ENSP00000398789.2	Q9Y5W8-2
	SNX13	ENST00000611725.4	TSL:1	c.13-11521A>T		intron	N/A	ENSP00000479044.1	A0A087WUZ7
	SNX13	ENST00000409604.1	TSL:1	c.13-11521A>T		intron	N/A	ENSP00000386639.1	Q9NSH0

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

African (AFR) AF: 0.485 AC: 20060 AN: 41344

American (AMR) AF: 0.429 AC: 6542 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1709 AN: 3462

East Asian (EAS) AF: 0.625 AC: 3222 AN: 5156

South Asian (SAS) AF: 0.665 AC: 3196 AN: 4804

European-Finnish (FIN) AF: 0.378 AC: 3984 AN: 10534

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26857 AN: 67908

Other (OTH) AF: 0.437 AC: 921 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.9
DANN	Benign	0.84
PhyloP100		-0.67
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: rs2691561; hg19: chr7-17948590;