7-17814952-GAAA-GAAAAAA

Position:

• chr7-17814952-GAAA-GAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_015132.5(SNX13):​c.1954-11_1954-9dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0020 (3 hom., cov: 0)
  • Exomes 𝑓: 0.043 (52 hom.)
• Consequence: SNX13 NM_015132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

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]

SNX13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX13	NM_015132.5	c.1954-11_1954-9dupTTT		intron_variant		ENST00000428135.7	NP_055947.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX13	ENST00000428135.7	c.1954-11_1954-9dupTTT		intron_variant		1	NM_015132.5	ENSP00000398789.2
SNX13	ENST00000611725.4	c.1987-11_1987-9dupTTT		intron_variant		1		ENSP00000479044.1
SNX13	ENST00000496855.1	n.298-11_298-9dupTTT		intron_variant		1
SNX13	ENST00000409076.6	n.*1652-11_*1652-9dupTTT		intron_variant		2		ENSP00000387053.2

Frequencies

GnomAD3 genomes AF: 0.00205 AC: 267 AN: 130340 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.00485

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00101

Gnomad ASJ AF: 0.000949

Gnomad EAS AF: 0.00107

Gnomad SAS AF: 0.00300

Gnomad FIN AF: 0.000487

Gnomad MID AF: 0.00365

Gnomad NFE AF: 0.000854

Gnomad OTH AF: 0.000563

GnomAD3 exomes AF: 0.0360 AC: 1227 AN: 34130 Hom.: 12 AF XY: 0.0381 AC XY: 726 AN XY: 19058

Gnomad AFR exome AF: 0.0544

Gnomad AMR exome AF: 0.0290

Gnomad ASJ exome AF: 0.0322

Gnomad EAS exome AF: 0.0498

Gnomad SAS exome AF: 0.0444

Gnomad FIN exome AF: 0.0233

Gnomad NFE exome AF: 0.0360

Gnomad OTH exome AF: 0.0359

GnomAD4 exome AF: 0.0429 AC: 46037 AN: 1072292 Hom.: 52 Cov.: 12 AF XY: 0.0435 AC XY: 22656 AN XY: 521270

Gnomad4 AFR exome AF: 0.0847

Gnomad4 AMR exome AF: 0.0426

Gnomad4 ASJ exome AF: 0.0464

Gnomad4 EAS exome AF: 0.0670

Gnomad4 SAS exome AF: 0.0694

Gnomad4 FIN exome AF: 0.0282

Gnomad4 NFE exome AF: 0.0403

Gnomad4 OTH exome AF: 0.0484

GnomAD4 genome AF: 0.00205 AC: 267 AN: 130354 Hom.: 3 Cov.: 0 AF XY: 0.00222 AC XY: 139 AN XY: 62478

Gnomad4 AFR AF: 0.00484

Gnomad4 AMR AF: 0.00101

Gnomad4 ASJ AF: 0.000949

Gnomad4 EAS AF: 0.00107

Gnomad4 SAS AF: 0.00302

Gnomad4 FIN AF: 0.000487

Gnomad4 NFE AF: 0.000854

Gnomad4 OTH AF: 0.000559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34649849; hg19: chr7-17854575;