20-46724875-CGGATGGATGGAT-CGGATGGATGGATGGATGGATGGAT

Variant names:

• chr20-46724875-C-CGGATGGATGGAT
• rs3092014
• NM_030777.4:c.5-147_5-136dupATGGATGGATGG

Variant summary

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

The NM_030777.4(SLC2A10):​c.5-147_5-136dupATGGATGGATGG 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 0.11 (2195 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-CGGATGGATGGAT is Benign according to our data. Variant chr20-46724875-C-CGGATGGATGGAT is described in ClinVar as [Benign]. Clinvar id is 1237574.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A10	NM_030777.4	c.5-147_5-136dupATGGATGGATGG		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_5-165insGGATGGATGGAT		intron_variant	Intron 1 of 4	1	NM_030777.4	ENSP00000352216.2
SLC2A10	ENST00000611837.1	n.157-166_157-165insGGATGGATGGAT		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.112 AC: 15622 AN: 139580 Hom.: 2187 Cov.: 0

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.0266

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0367

Gnomad MID AF: 0.0655

Gnomad NFE AF: 0.0204

Gnomad OTH AF: 0.0929

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

GnomAD4 genome AF: 0.112 AC: 15648 AN: 139694 Hom.: 2195 Cov.: 0 AF XY: 0.113 AC XY: 7676 AN XY: 67732

African (AFR) AF: 0.313 AC: 11343 AN: 36188

American (AMR) AF: 0.144 AC: 2060 AN: 14326

Ashkenazi Jewish (ASJ) AF: 0.0266 AC: 90 AN: 3386

East Asian (EAS) AF: 0.0409 AC: 183 AN: 4472

South Asian (SAS) AF: 0.0282 AC: 115 AN: 4080

European-Finnish (FIN) AF: 0.0367 AC: 326 AN: 8886

Middle Eastern (MID) AF: 0.0662 AC: 18 AN: 272

European-Non Finnish (NFE) AF: 0.0204 AC: 1333 AN: 65272

Other (OTH) AF: 0.0925 AC: 180 AN: 1946

Alfa AF: 0.0142 Hom.: 1700

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 14, 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;