Variant 7-17814952-G-GAA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_015132.5(SNX13):c.1954-9_1954-8insTT variant causes a splice polypyrimidine tract, 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 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.43

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX13	NM_015132.5 linkuse as main transcript	c.1954-9_1954-8insTT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000428135.7

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
SNX13	ENST00000428135.7 linkuse as main transcript	c.1954-9_1954-8insTT	splice_polypyrimidine_tract_variant, intron_variant	1	NM_015132.5	P1	Q9Y5W8-2
SNX13	ENST00000611725.4 linkuse as main transcript	c.1987-9_1987-8insTT	splice_polypyrimidine_tract_variant, intron_variant	1
SNX13	ENST00000496855.1 linkuse as main transcript	n.298-9_298-8insTT	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	1
SNX13	ENST00000409076.6 linkuse as main transcript	c.1652-9_1652-8insTT	splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.620

AC:

80554

AN:

129904

Hom.:

23900

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.302

AC:

10292

AN:

34130

Hom.:

717

AF XY:

0.296

AC XY:

5648

AN XY:

19058

show subpopulations

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 SAS exome

AF:

0.339

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.:

AF XY:

0.338

AC XY:

170246

AN XY:

503400

show subpopulations

Gnomad4 AFR exome

AF:

0.446

Gnomad4 AMR exome

AF:

0.334

Gnomad4 ASJ exome

AF:

0.337

Gnomad4 EAS exome

AF:

0.410

Gnomad4 SAS exome

AF:

0.355

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.336

Gnomad4 OTH exome

AF:

0.350

GnomAD4 genome

AF:

0.620

AC:

80554

AN:

129918

Hom.:

23898

Cov.:

AF XY:

0.620

AC XY:

38578

AN XY:

62226

show subpopulations

Gnomad4 AFR

AF:

0.739

Gnomad4 AMR

AF:

0.597

Gnomad4 ASJ

AF:

0.628

Gnomad4 EAS

AF:

0.731

Gnomad4 SAS

AF:

0.707

Gnomad4 FIN

AF:

0.450

Gnomad4 NFE

AF:

0.557

Gnomad4 OTH

AF:

0.581

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over