chr7-26371803-CT-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1

The NM_013322.3(SNX10):​c.312-8delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0123 in 1,218,084 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 33)
Exomes 𝑓: 0.014 ( 0 hom. )

Consequence

SNX10
NM_013322.3 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 7-26371803-CT-C is Benign according to our data. Variant chr7-26371803-CT-C is described in ClinVar as [Benign]. Clinvar id is 1991290.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0139 (14916/1069956) while in subpopulation AMR AF= 0.0174 (548/31472). AF 95% confidence interval is 0.0162. There are 0 homozygotes in gnomad4_exome. There are 7283 alleles in male gnomad4_exome subpopulation. Median coverage is 22. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SNX10NM_013322.3 linkc.312-8delT 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.312-8delT splice_region_variant, intron_variant Intron 5 of 6 1 NM_013322.3 ENSP00000343709.5 Q9Y5X0-1

Frequencies

GnomAD3 genomes
AF:
0.000162
AC:
24
AN:
148046
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000247
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000675
Gnomad ASJ
AF:
0.000294
Gnomad EAS
AF:
0.000196
Gnomad SAS
AF:
0.000213
Gnomad FIN
AF:
0.000921
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000135
Gnomad OTH
AF:
0.000495
GnomAD4 exome
AF:
0.0139
AC:
14916
AN:
1069956
Hom.:
0
Cov.:
22
AF XY:
0.0137
AC XY:
7283
AN XY:
531886
show subpopulations
Gnomad4 AFR exome
AF:
0.0138
Gnomad4 AMR exome
AF:
0.0174
Gnomad4 ASJ exome
AF:
0.0150
Gnomad4 EAS exome
AF:
0.00919
Gnomad4 SAS exome
AF:
0.0147
Gnomad4 FIN exome
AF:
0.0104
Gnomad4 NFE exome
AF:
0.0141
Gnomad4 OTH exome
AF:
0.0141
GnomAD4 genome
AF:
0.000162
AC:
24
AN:
148128
Hom.:
0
Cov.:
33
AF XY:
0.000208
AC XY:
15
AN XY:
72180
show subpopulations
Gnomad4 AFR
AF:
0.0000493
Gnomad4 AMR
AF:
0.0000674
Gnomad4 ASJ
AF:
0.000294
Gnomad4 EAS
AF:
0.000197
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000921
Gnomad4 NFE
AF:
0.000135
Gnomad4 OTH
AF:
0.000490
Alfa
AF:
0.0346
Hom.:
0

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jan 14, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

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