7-26371803-CTT-CTTTTTTTTTTTTTTTT

Variant names:

• chr7-26371803-C-CTTTTTTTTTTTTTT
• rs201825204
• NM_013322.3:c.312-8_312-7insTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_013322.3(SNX10):​c.312-8_312-7insTTTTTTTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000857 in 1,166,286 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 8.6e-7 (0 hom.)
• Consequence: SNX10 NM_013322.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013322.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX10	NM_013322.3	MANE Select	c.312-8_312-7insTTTTTTTTTTTTTT		splice_region intron	N/A	NP_037454.2
	SNX10	NM_001318198.1		c.390-8_390-7insTTTTTTTTTTTTTT		splice_region intron	N/A	NP_001305127.1	Q9Y5X0
	SNX10	NM_001362753.1		c.390-8_390-7insTTTTTTTTTTTTTT		splice_region intron	N/A	NP_001349682.1	B4DJM0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNX10	ENST00000338523.9	TSL:1 MANE Select	c.312-8_312-7insTTTTTTTTTTTTTT		splice_region intron	N/A	ENSP00000343709.5	Q9Y5X0-1
	SNX10	ENST00000396376.5	TSL:1	c.312-8_312-7insTTTTTTTTTTTTTT		splice_region intron	N/A	ENSP00000379661.1	Q9Y5X0-1
	SNX10	ENST00000446848.6	TSL:1	c.312-8_312-7insTTTTTTTTTTTTTT		splice_region intron	N/A	ENSP00000395474.3	Q9Y5X0-1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 8.57e-7 AC: 1 AN: 1166286 Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0 AN XY: 581156

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 26188

American (AMR) AF: 0.00 AC: 0 AN: 34578

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20274

East Asian (EAS) AF: 0.00 AC: 0 AN: 31986

South Asian (SAS) AF: 0.00 AC: 0 AN: 66104

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 43616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4830

European-Non Finnish (NFE) AF: 0.00000112 AC: 1 AN: 890788

Other (OTH) AF: 0.00 AC: 0 AN: 47922

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs201825204; hg19: chr7-26411423;