rs3091904

Variant names:

• chr20-46732816-T-C
• rs3091904
• NM_030777.4:c.1548-940T>C

Variant summary

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

The NM_030777.4(SLC2A10):​c.1548-940T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,846 control chromosomes in the GnomAD database, including 13,237 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 0.41 (13237 hom., cov: 31)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 7 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: PanelApp Australia, G2P, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Genomics England PanelApp

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 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.1548-940T>C		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.1548-940T>C		intron	N/A	ENSP00000352216.2	O95528
	SLC2A10	ENST00000862794.1		c.1842-940T>C		intron	N/A	ENSP00000532853.1
	SLC2A10	ENST00000862792.1		c.1680-940T>C		intron	N/A	ENSP00000532851.1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62427 AN: 151728 Hom.: 13212 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.412 AC: 62493 AN: 151846 Hom.: 13237 Cov.: 31 AF XY: 0.416 AC XY: 30886 AN XY: 74222

African (AFR) AF: 0.336 AC: 13887 AN: 41374

American (AMR) AF: 0.458 AC: 6998 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1546 AN: 3472

East Asian (EAS) AF: 0.602 AC: 3101 AN: 5152

South Asian (SAS) AF: 0.400 AC: 1920 AN: 4798

European-Finnish (FIN) AF: 0.456 AC: 4810 AN: 10544

Middle Eastern (MID) AF: 0.397 AC: 115 AN: 290

European-Non Finnish (NFE) AF: 0.425 AC: 28886 AN: 67932

Other (OTH) AF: 0.431 AC: 907 AN: 2106

Alfa AF: 0.415 Hom.: 6646

Bravo AF: 0.409

Asia WGS AF: 0.468 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.37
PhyloP100		-1.4
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

Other links and lift over

dbSNP: rs3091904; hg19: chr20-45361455;