7-26346087-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_013322.3(SNX10):c.-23-333C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,172 control chromosomes in the GnomAD database, including 1,232 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (1232 hom., cov: 31)
• Consequence: SNX10 NM_013322.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.171

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 7-26346087-C-T is Benign according to our data. Variant chr7-26346087-C-T is described in ClinVar as [Benign]. Clinvar id is 1239347.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX10	NM_013322.3	c.-23-333C>T		intron_variant		ENST00000338523.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX10	ENST00000338523.9	c.-23-333C>T		intron_variant		1	NM_013322.3	P1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18910 AN: 152054 Hom.: 1232 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.118

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.124 AC: 18925 AN: 152172 Hom.: 1232 Cov.: 31 AF XY: 0.125 AC XY: 9301 AN XY: 74410

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.118

Alfa AF: 0.126 Hom.: 251

Bravo AF: 0.128

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.43
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs12534819; hg19: chr7-26385707; COSMIC: COSV58402563;