chr7-26371803-CT-C

Variant names:

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

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.312-8delT 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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-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

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

Frequencies

GnomAD3 genomes AF: 0.000162 AC: 24 AN: 148046 Hom.: 0 Cov.: 33

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

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

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

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

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs201825204; hg19: chr7-26411423;