rs2425902

Variant names:

• chr20-46721941-A-G
• rs2425902
• NM_030777.4:c.5-3100A>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.5-3100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,120 control chromosomes in the GnomAD database, including 7,044 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 0.28 (7044 hom., cov: 32)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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.5-3100A>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.5-3100A>G		intron	N/A	ENSP00000352216.2	O95528
	SLC2A10	ENST00000862794.1		c.299-3100A>G		intron	N/A	ENSP00000532853.1
	SLC2A10	ENST00000862792.1		c.5-3100A>G		intron	N/A	ENSP00000532851.1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42662 AN: 152002 Hom.: 7039 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.281 AC: 42671 AN: 152120 Hom.: 7044 Cov.: 32 AF XY: 0.286 AC XY: 21248 AN XY: 74360

African (AFR) AF: 0.106 AC: 4416 AN: 41526

American (AMR) AF: 0.385 AC: 5880 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1313 AN: 3462

East Asian (EAS) AF: 0.580 AC: 2997 AN: 5168

South Asian (SAS) AF: 0.303 AC: 1459 AN: 4816

European-Finnish (FIN) AF: 0.321 AC: 3393 AN: 10584

Middle Eastern (MID) AF: 0.321 AC: 93 AN: 290

European-Non Finnish (NFE) AF: 0.326 AC: 22188 AN: 67972

Other (OTH) AF: 0.326 AC: 690 AN: 2116

Alfa AF: 0.310 Hom.: 3986

Bravo AF: 0.281

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.44
PhyloP100		0.65
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: rs2425902;

hg19: chr20-45350580;