7-26371803-CTT-CT
Variant names:
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
NM_013322.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.492
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]
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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 |
---|---|---|---|---|---|---|---|---|
SNX10 | NM_013322.3 | c.312-8delT | splice_region_variant, intron_variant | Intron 5 of 6 | ENST00000338523.9 | NP_037454.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000162 AC: 24AN: 148046Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0139 AC: 14916AN: 1069956Hom.: 0 Cov.: 22 AF XY: 0.0137 AC XY: 7283AN XY: 531886
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GnomAD4 genome AF: 0.000162 AC: 24AN: 148128Hom.: 0 Cov.: 33 AF XY: 0.000208 AC XY: 15AN XY: 72180
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at