Genetic Variant SNX10:c.312-8delT (chr7-26371803-CT-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.492

Variant links:

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 links:

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

SNX10-AS1 links:

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ACMG classification

Classification made for transcript

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 link	c.312-8delT		splice_region_variant, intron_variant	Intron 5 of 6	ENST00000338523.9	NP_037454.2	Q9Y5X0-1A0A024RA70Q8N5Z3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNX10	ENST00000338523.9 link	c.312-8delT		splice_region_variant, intron_variant	Intron 5 of 6	1	NM_013322.3	ENSP00000343709.5		Q9Y5X0-1

Frequencies

GnomAD3 genomes

AF:

0.000162

AC:

AN:

148046

Hom.:

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.0137

AC XY:

7283

AN XY:

531886

show subpopulations

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:

AN:

148128

Hom.:

Cov.:

AF XY:

0.000208

AC XY:

AN XY:

72180

show subpopulations

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.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

7-26371803-CTT-CT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over