20-46724806-AGGAT-A

Variant names:

• chr20-46724806-AGGAT-A
• rs111504264
• NM_030777.4:c.5-196_5-193delATGG

Variant summary

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

The NM_030777.4(SLC2A10):​c.5-196_5-193delATGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 125,634 control chromosomes in the GnomAD database, including 92 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.031 (92 hom., cov: 26)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00
• 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 20-46724806-AGGAT-A is Benign according to our data. Variant chr20-46724806-AGGAT-A is described in ClinVar as [Benign]. Clinvar id is 1270430.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A10	NM_030777.4	c.5-196_5-193delATGG		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.5-234_5-231delGGAT		intron_variant	Intron 1 of 4	1	NM_030777.4	ENSP00000352216.2
SLC2A10	ENST00000611837.1	n.157-234_157-231delGGAT		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 3838 AN: 125508 Hom.: 92 Cov.: 26

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0261

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0388

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0306 AC: 3846 AN: 125634 Hom.: 92 Cov.: 26 AF XY: 0.0307 AC XY: 1862 AN XY: 60746

African (AFR) AF: 0.0692 AC: 2228 AN: 32214

American (AMR) AF: 0.0178 AC: 227 AN: 12762

Ashkenazi Jewish (ASJ) AF: 0.0261 AC: 84 AN: 3218

East Asian (EAS) AF: 0.0200 AC: 72 AN: 3602

South Asian (SAS) AF: 0.0181 AC: 60 AN: 3316

European-Finnish (FIN) AF: 0.0359 AC: 273 AN: 7610

Middle Eastern (MID) AF: 0.0309 AC: 6 AN: 194

European-Non Finnish (NFE) AF: 0.0137 AC: 826 AN: 60160

Other (OTH) AF: 0.0240 AC: 43 AN: 1788

Alfa AF: 0.00890 Hom.: 16

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 06, 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		0.0
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs111504264; hg19: chr20-45353445;