rs2425904

Variant names:

• chr20-46728237-C-T
• rs2425904
• NM_030777.4:c.1412-1116C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-46728237-C-T
• chr20-46728237-C-A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_030777.4(SLC2A10):​c.1412-1116C>T 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 152,064 control chromosomes in the GnomAD database, including 7,041 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (7041 hom., cov: 32)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0870
• Publications: 5 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 20-46728237-C-T is Benign according to our data. Variant chr20-46728237-C-T is described in ClinVar as Benign. ClinVar VariationId is 3894759.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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.1412-1116C>T		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.1412-1116C>T		intron	N/A	ENSP00000352216.2	O95528
	SLC2A10	ENST00000862792.1		c.1461C>T	p.Ser487Ser	synonymous	Exon 4 of 6	ENSP00000532851.1
	SLC2A10	ENST00000862794.1		c.1706-1116C>T		intron	N/A	ENSP00000532853.1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42649 AN: 151946 Hom.: 7036 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.281 AC: 42658 AN: 152064 Hom.: 7041 Cov.: 32 AF XY: 0.286 AC XY: 21245 AN XY: 74324

African (AFR) AF: 0.107 AC: 4430 AN: 41510

American (AMR) AF: 0.385 AC: 5884 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3468

East Asian (EAS) AF: 0.582 AC: 3001 AN: 5160

South Asian (SAS) AF: 0.303 AC: 1460 AN: 4814

European-Finnish (FIN) AF: 0.320 AC: 3379 AN: 10568

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22168 AN: 67960

Other (OTH) AF: 0.325 AC: 686 AN: 2108

Alfa AF: 0.278 Hom.: 847

Bravo AF: 0.282

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.2
DANN	Benign	0.62
PhyloP100		0.087
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs2425904; hg19: chr20-45356876;