Genetic Variant SNX13:c.1954-11_1954-9delTTT (chr7-17814952-GAAA-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

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. There is a variant allele frequency bias in the population database for this variant (GnomAdExome4), which may indicate mosaicism or somatic mutations in the reference population data. 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

Publications

0 publications found

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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX13	NM_015132.5 link	c.1954-11_1954-9delTTT		intron_variant	Intron 19 of 25	ENST00000428135.7	NP_055947.1	Q9Y5W8-2A0A024R9Z9Q86XC4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SNX13	ENST00000428135.7 link	c.1954-11_1954-9delTTT	intron_variant	Intron 19 of 25	1	NM_015132.5	ENSP00000398789.2	Q9Y5W8-2
SNX13	ENST00000611725.4 link	c.1987-11_1987-9delTTT	intron_variant	Intron 19 of 24	1		ENSP00000479044.1	A0A087WUZ7
SNX13	ENST00000496855.1 link	n.298-11_298-9delTTT	intron_variant	Intron 2 of 8	1
SNX13	ENST00000409076.6 link	n.1652-11_1652-9delTTT	intron_variant	Intron 20 of 26	2		ENSP00000387053.2	F8W8A9

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

130362

Hom.:

Cov.:

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.:

AF XY:

0.000124

AC XY:

AN XY:

530932

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000143

AC:

AN:

21020

American (AMR)

AF:

0.000207

AC:

AN:

9684

Ashkenazi Jewish (ASJ)

AF:

0.000117

AC:

AN:

17102

East Asian (EAS)

AF:

0.0000805

AC:

AN:

24858

South Asian (SAS)

AF:

0.000197

AC:

AN:

40604

European-Finnish (FIN)

AF:

0.000388

AC:

AN:

30966

Middle Eastern (MID)

AF:

0.000236

AC:

AN:

4234

European-Non Finnish (NFE)

AF:

0.0000868

AC:

AN:

898944

Other (OTH)

AF:

0.0000897

AC:

AN:

44592

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.245

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

130362

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

62468

African (AFR)

AF:

0.00

AC:

AN:

36528

American (AMR)

AF:

0.00

AC:

AN:

12904

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3160

East Asian (EAS)

AF:

0.00

AC:

AN:

4686

South Asian (SAS)

AF:

0.00

AC:

AN:

4330

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6160

Middle Eastern (MID)

AF:

0.00

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

59764

Other (OTH)

AF:

0.00

AC:

AN:

1776

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.5

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over