rs34649849

Positions:

• chr7-17814952-GAAA-G
• chr7-17814952-GAAA-GA
• chr7-17814952-GAAA-GAA
• chr7-17814952-GAAA-GAAAA
• chr7-17814952-GAAA-GAAAAA
• chr7-17814952-GAAA-GAAAAAA
• chr7-17814952-GAAA-GAAAAAAA
• chr7-17814952-GAAA-GAAAAAAAA
• chr7-17814952-GAAA-GAAAAAAAAAAAAA
• chr7-17814952-GAAA-GAAAAAAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_015132.5(SNX13):​c.1954-11_1954-9delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,092,004 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00010 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SNX13 NM_015132.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 112 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 130362 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000103 AC: 112 AN: 1092004 Hom.: 0 AF XY: 0.000124 AC XY: 66 AN XY: 530932

Gnomad4 AFR exome AF: 0.000143

Gnomad4 AMR exome AF: 0.000207

Gnomad4 ASJ exome AF: 0.000117

Gnomad4 EAS exome AF: 0.0000805

Gnomad4 SAS exome AF: 0.000197

Gnomad4 FIN exome AF: 0.000388

Gnomad4 NFE exome AF: 0.0000868

Gnomad4 OTH exome AF: 0.0000897

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 130362 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 62468

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-17854575;