Genetic Variant SNX14:c.2654-266_2654-262dupTTTTT (chr6-85508320-T-TAAAAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_153816.6(SNX14):c.2654-266_2654-262dupTTTTT 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: 31)

Exomes 𝑓: 0.0000013 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SNX14
NM_153816.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.381

Publications

0 publications found

Variant links:

Genes affected

SNX14 (HGNC:14977): (sorting nexin 14) This gene encodes a member of the sorting nexin family. Members of this family have a phox (PX) phosphoinositide binding domain and are involved in intracellular trafficking. The encoded protein also contains a regulator of G protein signaling (RGS) domain. Regulator of G protein signaling family members are regulatory molecules that act as GTPase activating proteins for G alpha subunits of heterotrimeric G proteins. Alternate splicing results in transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]

SNX14 Gene-Disease associations (from GenCC):

autosomal recessive spinocerebellar ataxia 20
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, G2P, Ambry Genetics, PanelApp Australia

SNX14 links:

ENSG00000271793 (HGNC:):

ENSG00000271793 links:

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ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153816.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SNX14	NM_153816.6	MANE Select	c.2654-266_2654-262dupTTTTT	intron	N/A	NP_722523.1	Q9Y5W7-1
SNX14	NM_001350532.2		c.2717-266_2717-262dupTTTTT	intron	N/A	NP_001337461.1	A0A804HKZ1
SNX14	NM_001350533.2		c.2651-266_2651-262dupTTTTT	intron	N/A	NP_001337462.1	A0A804HKC6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SNX14	ENST00000314673.8	TSL:1 MANE Select	c.2654-266_2654-262dupTTTTT	intron	N/A	ENSP00000313121.3	Q9Y5W7-1
SNX14	ENST00000369627.6	TSL:1	c.2627-266_2627-262dupTTTTT	intron	N/A	ENSP00000358641.2	Q9Y5W7-4
SNX14	ENST00000346348.7	TSL:1	c.2495-266_2495-262dupTTTTT	intron	N/A	ENSP00000257769.3	Q9Y5W7-2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

99030

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:

0.00000130

AC:

AN:

770156

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

357830

show subpopulations

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

African (AFR)

AF:

0.00

AC:

AN:

14394

American (AMR)

AF:

0.00

AC:

AN:

1228

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

5170

East Asian (EAS)

AF:

0.00

AC:

AN:

4350

South Asian (SAS)

AF:

0.00

AC:

AN:

15260

European-Finnish (FIN)

AF:

0.00

AC:

AN:

986

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1568

European-Non Finnish (NFE)

AF:

0.00000143

AC:

AN:

701616

Other (OTH)

AF:

0.00

AC:

AN:

25584

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.275

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:

99030

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

46988

African (AFR)

AF:

0.00

AC:

AN:

27162

American (AMR)

AF:

0.00

AC:

AN:

9144

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2414

East Asian (EAS)

AF:

0.00

AC:

AN:

3818

South Asian (SAS)

AF:

0.00

AC:

AN:

3274

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4754

Middle Eastern (MID)

AF:

0.00

AC:

AN:

184

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

46300

Other (OTH)

AF:

0.00

AC:

AN:

1352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.38

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over