chr7-17814952-G-GAA

Variant names:

• chr7-17814952-G-GAA
• rs34649849
• NM_015132.5:c.1954-10_1954-9dupTT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015132.5(SNX13):​c.1954-10_1954-9dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.62 (23898 hom., cov: 0)
  • Exomes 𝑓: 0.34 (7097 hom.)
  • Failed GnomAD Quality Control
• Consequence: SNX13 NM_015132.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.43
• Publications: 2 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 -10 ACMG points.

• BP6: Variant 7-17814952-G-GAA is Benign according to our data. Variant chr7-17814952-G-GAA is described in ClinVar as Benign. ClinVar VariationId is 403464.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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.1954-10_1954-9dupTT		intron	N/A	NP_055947.1	Q9Y5W8-2
	SNX13	NM_001350862.2		c.1987-10_1987-9dupTT		intron	N/A	NP_001337791.1	Q9Y5W8-1
	SNX13	NM_001350863.2		c.1714-10_1714-9dupTT		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.1954-9_1954-8insTT		intron	N/A	ENSP00000398789.2	Q9Y5W8-2
	SNX13	ENST00000611725.4	TSL:1	c.1987-9_1987-8insTT		intron	N/A	ENSP00000479044.1	A0A087WUZ7
	SNX13	ENST00000496855.1	TSL:1	n.298-9_298-8insTT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 80554 AN: 129904 Hom.: 23900 Cov.: 0

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.579

GnomAD2 exomes AF: 0.302 AC: 10292 AN: 34130 AF XY: 0.296

Gnomad AFR exome AF: 0.467

Gnomad AMR exome AF: 0.265

Gnomad ASJ exome AF: 0.283

Gnomad EAS exome AF: 0.340

Gnomad FIN exome AF: 0.234

Gnomad NFE exome AF: 0.299

Gnomad OTH exome AF: 0.306

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.339 AC: 350628 AN: 1034566 Hom.: 7097 Cov.: 12 AF XY: 0.338 AC XY: 170246 AN XY: 503400

African (AFR) AF: 0.446 AC: 9070 AN: 20320

American (AMR) AF: 0.334 AC: 3100 AN: 9294

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 5508 AN: 16342

East Asian (EAS) AF: 0.410 AC: 9754 AN: 23780

South Asian (SAS) AF: 0.355 AC: 14049 AN: 39544

European-Finnish (FIN) AF: 0.250 AC: 7462 AN: 29864

Middle Eastern (MID) AF: 0.411 AC: 1658 AN: 4038

European-Non Finnish (NFE) AF: 0.336 AC: 285149 AN: 848926

Other (OTH) AF: 0.350 AC: 14878 AN: 42458

GnomAD4 genome AF: 0.620 AC: 80554 AN: 129918 Hom.: 23898 Cov.: 0 AF XY: 0.620 AC XY: 38578 AN XY: 62226

African (AFR) AF: 0.739 AC: 26944 AN: 36464

American (AMR) AF: 0.597 AC: 7675 AN: 12852

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 1978 AN: 3152

East Asian (EAS) AF: 0.731 AC: 3410 AN: 4666

South Asian (SAS) AF: 0.707 AC: 3036 AN: 4292

European-Finnish (FIN) AF: 0.450 AC: 2737 AN: 6088

Middle Eastern (MID) AF: 0.659 AC: 166 AN: 252

European-Non Finnish (NFE) AF: 0.557 AC: 33217 AN: 59590

Other (OTH) AF: 0.581 AC: 1036 AN: 1784

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs34649849; hg19: chr7-17854575;