7-26346206-T-G

Position:

• chr7-26346206-T-G

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.-23-214T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,020 control chromosomes in the GnomAD database, including 3,630 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.20 (3630 hom., cov: 31)
• Consequence: SNX10 NM_013322.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.251

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 7-26346206-T-G is Benign according to our data. Variant chr7-26346206-T-G is described in ClinVar as [Benign]. Clinvar id is 1286408.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNX10	NM_013322.3	c.-23-214T>G		intron_variant		ENST00000338523.9	NP_037454.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNX10	ENST00000338523.9	c.-23-214T>G		intron_variant		1	NM_013322.3	ENSP00000343709.5

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30925 AN: 151902 Hom.: 3618 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.204 AC: 30961 AN: 152020 Hom.: 3630 Cov.: 31 AF XY: 0.208 AC XY: 15429 AN XY: 74304

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.193

Alfa AF: 0.126 Hom.: 293

Bravo AF: 0.213

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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.89
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs10951130; hg19: chr7-26385826; COSMIC: COSV58401334;