20-46724875-C-CGGATGGATGGATGGAT

Variant names:

• chr20-46724875-C-CGGATGGATGGATGGAT
• rs3092014
• NM_030777.4:c.5-151_5-136dupATGGATGGATGGATGG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_030777.4(SLC2A10):​c.5-151_5-136dupATGGATGGATGGATGG variant causes a intron change involving the alteration of a non-conserved nucleotide. 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. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.052 (298 hom., cov: 0)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.234
• Publications: 0 publications found

Genes affected

SLC2A10 (HGNC:13444): (solute carrier family 2 member 10) This gene encodes a member of the class III facilitative glucose transporter family. The encoded protein plays a role in regulation of glucose homeostasis. Mutations in this gene have been associated with arterial tortuosity syndrome.[provided by RefSeq, Dec 2009]

SLC2A10 Gene-Disease associations (from GenCC):

• arterial tortuosity syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, G2P
• familial thoracic aortic aneurysm and aortic dissection

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 20-46724875-C-CGGATGGATGGATGGAT is Benign according to our data. Variant chr20-46724875-C-CGGATGGATGGATGGAT is described in ClinVar as [Benign]. Clinvar id is 1241818.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A10	NM_030777.4	c.5-151_5-136dupATGGATGGATGGATGG		intron_variant	Intron 1 of 4	ENST00000359271.4	NP_110404.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A10	ENST00000359271.4	c.5-166_5-165insGGATGGATGGATGGAT		intron_variant	Intron 1 of 4	1	NM_030777.4	ENSP00000352216.2
SLC2A10	ENST00000611837.1	n.157-166_157-165insGGATGGATGGATGGAT		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0518 AC: 7228 AN: 139616 Hom.: 295 Cov.: 0

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.0359

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0536

Gnomad MID AF: 0.0483

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0518 AC: 7243 AN: 139732 Hom.: 298 Cov.: 0 AF XY: 0.0519 AC XY: 3518 AN XY: 67756

African (AFR) AF: 0.0751 AC: 2722 AN: 36232

American (AMR) AF: 0.0274 AC: 393 AN: 14342

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 128 AN: 3386

East Asian (EAS) AF: 0.0729 AC: 326 AN: 4474

South Asian (SAS) AF: 0.111 AC: 452 AN: 4068

European-Finnish (FIN) AF: 0.0536 AC: 477 AN: 8894

Middle Eastern (MID) AF: 0.0441 AC: 12 AN: 272

European-Non Finnish (NFE) AF: 0.0398 AC: 2598 AN: 65250

Other (OTH) AF: 0.0533 AC: 104 AN: 1950

Alfa AF: 0.0524 Hom.: 1700

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 10, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs3092014; hg19: chr20-45353514;