7-26371803-C-CT

Variant names:

• chr7-26371803-C-CT
• rs201825204
• NM_013322.3:c.312-8dupT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2 BP6_Moderate BS1

The NM_013322.3(SNX10):​c.312-8dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0039 in 1,285,996 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 0.00076 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0043 (0 hom.)
• Consequence: SNX10 NM_013322.3 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:2
• 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]

SNX10-AS1 (HGNC:55845): (SNX10 antisense RNA 1)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 7-26371803-C-CT is Benign according to our data. Variant chr7-26371803-C-CT is described in ClinVar as [Benign]. Clinvar id is 1533579.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000755 (112/148266) while in subpopulation EAS AF= 0.00335 (17/5080). AF 95% confidence interval is 0.00213. There are 0 homozygotes in gnomad4. There are 51 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNX10	NM_013322.3	c.312-8dupT		splice_region_variant, intron_variant	Intron 5 of 6	ENST00000338523.9	NP_037454.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX10	ENST00000338523.9	c.312-8dupT		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_013322.3	ENSP00000343709.5

Frequencies

GnomAD3 genomes AF: 0.000749 AC: 111 AN: 148184 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00136

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00128

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00334

Gnomad SAS AF: 0.000639

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000255

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00431 AC: 4906 AN: 1137730 Hom.: 0 Cov.: 22 AF XY: 0.00400 AC XY: 2266 AN XY: 567132

Gnomad4 AFR exome AF: 0.00501

Gnomad4 AMR exome AF: 0.00358

Gnomad4 ASJ exome AF: 0.00279

Gnomad4 EAS exome AF: 0.00912

Gnomad4 SAS exome AF: 0.00408

Gnomad4 FIN exome AF: 0.00192

Gnomad4 NFE exome AF: 0.00435

Gnomad4 OTH exome AF: 0.00361

GnomAD4 genome AF: 0.000755 AC: 112 AN: 148266 Hom.: 0 Cov.: 33 AF XY: 0.000706 AC XY: 51 AN XY: 72268

Gnomad4 AFR AF: 0.00138

Gnomad4 AMR AF: 0.00128

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00335

Gnomad4 SAS AF: 0.000641

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000255

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

SNX10-related disorder Benign:1

May 14, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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

Other links and lift over

dbSNP: rs201825204; hg19: chr7-26411423;