7-17897956-A-G

Variant names:

• chr7-17897956-A-G
• rs1568818
• NM_015132.5:c.13-510T>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.13-510T>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
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX13	NM_015132.5	MANE Select	c.13-510T>C		intron	N/A	NP_055947.1
	SNX13	NM_001350862.2		c.13-510T>C		intron	N/A	NP_001337791.1
	SNX13	NM_001350863.2		c.-221-510T>C		intron	N/A	NP_001337792.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX13	ENST00000428135.7	TSL:1 MANE Select	c.13-510T>C		intron	N/A	ENSP00000398789.2
	SNX13	ENST00000611725.4	TSL:1	c.13-510T>C		intron	N/A	ENSP00000479044.1
	SNX13	ENST00000409604.1	TSL:1	c.13-510T>C		intron	N/A	ENSP00000386639.1

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

African (AFR) AF: 0.490 AC: 20234 AN: 41334

American (AMR) AF: 0.454 AC: 6910 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1677 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3234 AN: 5144

South Asian (SAS) AF: 0.655 AC: 3154 AN: 4814

European-Finnish (FIN) AF: 0.376 AC: 3930 AN: 10464

Middle Eastern (MID) AF: 0.490 AC: 142 AN: 290

European-Non Finnish (NFE) AF: 0.394 AC: 26727 AN: 67776

Other (OTH) AF: 0.440 AC: 926 AN: 2106

Alfa AF: 0.423 Hom.: 1780

Bravo AF: 0.452

Asia WGS AF: 0.645 AC: 2227 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.30
PhyloP100		-0.41
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: rs1568818; hg19: chr7-17937579;