Genetic Variant NM_015132.5:c.1954-15_1954-9dupTTTTTTT (chr7-17814952-G-GAAAAAAA) – 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.1954-15_1954-9dupTTTTTTT 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 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SNX13
NM_015132.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43

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.1954-15_1954-9dupTTTTTTT		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.1954-9_1954-8insTTTTTTT	intron_variant	Intron 19 of 25	1	NM_015132.5	ENSP00000398789.2	Q9Y5W8-2
SNX13	ENST00000611725.4 link	c.1987-9_1987-8insTTTTTTT	intron_variant	Intron 19 of 24	1		ENSP00000479044.1	A0A087WUZ7
SNX13	ENST00000496855.1 link	n.298-9_298-8insTTTTTTT	intron_variant	Intron 2 of 8	1
SNX13	ENST00000409076.6 link	n.1652-9_1652-8insTTTTTTT	intron_variant	Intron 20 of 26	2		ENSP00000387053.2	F8W8A9

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

130360

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:

0.00000274

AC:

AN:

1092902

Hom.:

Cov.:

AF XY:

0.00000188

AC XY:

AN XY:

531382

show subpopulations

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

African (AFR)

AF:

0.0000476

AC:

AN:

21030

American (AMR)

AF:

0.00

AC:

AN:

9690

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17126

East Asian (EAS)

AF:

0.00

AC:

AN:

24868

South Asian (SAS)

AF:

0.0000246

AC:

AN:

40670

European-Finnish (FIN)

AF:

0.00

AC:

AN:

31040

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4236

European-Non Finnish (NFE)

AF:

0.00000111

AC:

AN:

899600

Other (OTH)

AF:

0.00

AC:

AN:

44642

⚠️ 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: 0.258

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:

130360

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

62466

African (AFR)

AF:

0.00

AC:

AN:

36526

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

1.4

Splicing

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