7-26346534-T-C

Position:

• chr7-26346534-T-C

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.24+68T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 1,217,994 control chromosomes in the GnomAD database, including 88,409 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.43 (16037 hom., cov: 32)
  • Exomes 𝑓: 0.35 (72372 hom.)
• Consequence: SNX10 NM_013322.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0470

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=-0.92).
• BP6: Variant 7-26346534-T-C is Benign according to our data. Variant chr7-26346534-T-C is described in ClinVar as [Benign]. Clinvar id is 1221420.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNX10	NM_013322.3	c.24+68T>C		intron_variant		ENST00000338523.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNX10	ENST00000338523.9	c.24+68T>C		intron_variant		1	NM_013322.3	P1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65913 AN: 151958 Hom.: 15987 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.443

GnomAD4 exome AF: 0.353 AC: 376582 AN: 1065918 Hom.: 72372 AF XY: 0.363 AC XY: 199176 AN XY: 548818

Gnomad4 AFR exome AF: 0.648

Gnomad4 AMR exome AF: 0.436

Gnomad4 ASJ exome AF: 0.482

Gnomad4 EAS exome AF: 0.470

Gnomad4 SAS exome AF: 0.599

Gnomad4 FIN exome AF: 0.295

Gnomad4 NFE exome AF: 0.304

Gnomad4 OTH exome AF: 0.389

GnomAD4 genome AF: 0.434 AC: 66028 AN: 152076 Hom.: 16037 Cov.: 32 AF XY: 0.437 AC XY: 32463 AN XY: 74364

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.441

Alfa AF: 0.370 Hom.: 6218

Bravo AF: 0.451

Asia WGS AF: 0.542 AC: 1883 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.66

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: rs3801890; hg19: chr7-26386154; COSMIC: COSV58402171;