NM_013322.3:c.312-9_312-8dupTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_013322.3(SNX10):​c.312-9_312-8dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000609 in 1,314,170 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000067 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000060 ( 0 hom. )

Consequence

SNX10
NM_013322.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.492
Variant links:
Genes affected
SNX10 (HGNC:14974): (sorting nexin 10) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like some family members. This gene may play a role in regulating endosome homeostasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]
SNX10-AS1 (HGNC:55845): (SNX10 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNX10NM_013322.3 linkc.312-9_312-8dupTT splice_region_variant, intron_variant Intron 5 of 6 ENST00000338523.9 NP_037454.2 Q9Y5X0-1A0A024RA70Q8N5Z3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SNX10ENST00000338523.9 linkc.312-9_312-8dupTT splice_region_variant, intron_variant Intron 5 of 6 1 NM_013322.3 ENSP00000343709.5 Q9Y5X0-1

Frequencies

GnomAD3 genomes
AF:
0.00000675
AC:
1
AN:
148194
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000247
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:
0.00000600
AC:
7
AN:
1165976
Hom.:
0
Cov.:
22
AF XY:
0.00000516
AC XY:
3
AN XY:
581008
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000289
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000313
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000229
Gnomad4 NFE exome
AF:
0.00000337
Gnomad4 OTH exome
AF:
0.0000209
GnomAD4 genome
AF:
0.00000675
AC:
1
AN:
148194
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
72182
show subpopulations
Gnomad4 AFR
AF:
0.0000247
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

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.

Other links and lift over

dbSNP: rs201825204; hg19: chr7-26411423; API