rs2425906

Variant names:

• chr20-46729506-T-G
• rs2425906
• NM_030777.4:c.1547+18T>G

Your query was ambiguous. Multiple possible variants found:

• chr20-46729506-T-G
• chr20-46729506-T-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_030777.4(SLC2A10):​c.1547+18T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 1,611,072 control chromosomes in the GnomAD database, including 141,855 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.38 (11570 hom., cov: 31)
  • Exomes 𝑓: 0.42 (130285 hom.)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:8
• Conservation: PhyloP100: -2.87
• Publications: 8 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 20-46729506-T-G is Benign according to our data. Variant chr20-46729506-T-G is described in ClinVar as Benign. ClinVar VariationId is 139178.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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.1547+18T>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.1547+18T>G		intron	N/A	ENSP00000352216.2	O95528
	SLC2A10	ENST00000862794.1		c.1841+18T>G		intron	N/A	ENSP00000532853.1
	SLC2A10	ENST00000862792.1		c.1679+18T>G		intron	N/A	ENSP00000532851.1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 56918 AN: 151560 Hom.: 11559 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.359

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.406

GnomAD2 exomes AF: 0.418 AC: 104878 AN: 250922 AF XY: 0.417

Gnomad AFR exome AF: 0.216

Gnomad AMR exome AF: 0.422

Gnomad ASJ exome AF: 0.440

Gnomad EAS exome AF: 0.607

Gnomad FIN exome AF: 0.449

Gnomad NFE exome AF: 0.426

Gnomad OTH exome AF: 0.420

GnomAD4 exome AF: 0.418 AC: 610606 AN: 1459404 Hom.: 130285 Cov.: 38 AF XY: 0.416 AC XY: 302134 AN XY: 726134

African (AFR) AF: 0.210 AC: 7015 AN: 33434

American (AMR) AF: 0.423 AC: 18887 AN: 44696

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 11360 AN: 26116

East Asian (EAS) AF: 0.601 AC: 23832 AN: 39662

South Asian (SAS) AF: 0.346 AC: 29846 AN: 86180

European-Finnish (FIN) AF: 0.443 AC: 23611 AN: 53302

Middle Eastern (MID) AF: 0.367 AC: 2112 AN: 5748

European-Non Finnish (NFE) AF: 0.422 AC: 468848 AN: 1109966

Other (OTH) AF: 0.416 AC: 25095 AN: 60300

GnomAD4 genome AF: 0.376 AC: 56954 AN: 151668 Hom.: 11570 Cov.: 31 AF XY: 0.380 AC XY: 28180 AN XY: 74064

African (AFR) AF: 0.219 AC: 9067 AN: 41338

American (AMR) AF: 0.446 AC: 6809 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1484 AN: 3472

East Asian (EAS) AF: 0.599 AC: 3085 AN: 5146

South Asian (SAS) AF: 0.341 AC: 1635 AN: 4794

European-Finnish (FIN) AF: 0.459 AC: 4800 AN: 10460

Middle Eastern (MID) AF: 0.379 AC: 110 AN: 290

European-Non Finnish (NFE) AF: 0.424 AC: 28787 AN: 67912

Other (OTH) AF: 0.408 AC: 857 AN: 2102

Alfa AF: 0.323 Hom.: 1494

Bravo AF: 0.370

Asia WGS AF: 0.426 AC: 1478 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	5	not specified (5)
-	-	2	Arterial tortuosity syndrome (2)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.027
DANN	Benign	0.58
PhyloP100		-2.9
Mutation Taster		=9/91	disease causing

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: rs2425906;

hg19: chr20-45358145;

COSMIC: COSV63714393;

COSMIC: COSV63714393;