chr20-46727347-A-G

Variant names:

• chr20-46727347-A-G
• rs2076293
• NM_030777.4:c.1411+361A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030777.4(SLC2A10):​c.1411+361A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,782 control chromosomes in the GnomAD database, including 21,162 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (21162 hom., cov: 31)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 4 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, PanelApp Australia, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen, G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030777.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A10	NM_030777.4	MANE Select	c.1411+361A>G		intron	N/A	NP_110404.1	O95528

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A10	ENST00000359271.4	TSL:1 MANE Select	c.1411+361A>G		intron	N/A	ENSP00000352216.2	O95528
	SLC2A10	ENST00000862794.1		c.1705+361A>G		intron	N/A	ENSP00000532853.1
	SLC2A10	ENST00000862792.1		c.1392+361A>G		intron	N/A	ENSP00000532851.1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79389 AN: 151662 Hom.: 21115 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.524 AC: 79484 AN: 151782 Hom.: 21162 Cov.: 31 AF XY: 0.529 AC XY: 39224 AN XY: 74152

African (AFR) AF: 0.573 AC: 23699 AN: 41382

American (AMR) AF: 0.604 AC: 9201 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1675 AN: 3462

East Asian (EAS) AF: 0.689 AC: 3561 AN: 5166

South Asian (SAS) AF: 0.488 AC: 2340 AN: 4794

European-Finnish (FIN) AF: 0.530 AC: 5559 AN: 10498

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31833 AN: 67920

Other (OTH) AF: 0.531 AC: 1120 AN: 2110

Alfa AF: 0.478 Hom.: 2145

Bravo AF: 0.531

Asia WGS AF: 0.583 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.79
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2076293;

hg19: chr20-45355986;