NM_030777.4:c.4+2513A>T

Variant names:

• chr20-46712253-A-T
• rs2425897
• NM_030777.4:c.4+2513A>T

Variant summary

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

The NM_030777.4(SLC2A10):​c.4+2513A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.98 in 152,328 control chromosomes in the GnomAD database, including 73,119 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 0.98 (73119 hom., cov: 31)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 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 = 0.987 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.4+2513A>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.4+2513A>T		intron	N/A	ENSP00000352216.2	O95528
	SLC2A10	ENST00000862794.1		c.298+2219A>T		intron	N/A	ENSP00000532853.1
	SLC2A10	ENST00000862792.1		c.4+2513A>T		intron	N/A	ENSP00000532851.1

Frequencies

GnomAD3 genomes AF: 0.980 AC: 149104 AN: 152210 Hom.: 73059 Cov.: 31

Gnomad AFR AF: 0.995

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.972

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

GnomAD4 genome AF: 0.980 AC: 149223 AN: 152328 Hom.: 73119 Cov.: 31 AF XY: 0.981 AC XY: 73024 AN XY: 74474

African (AFR) AF: 0.995 AC: 41361 AN: 41566

American (AMR) AF: 0.974 AC: 14917 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3328 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5178

South Asian (SAS) AF: 0.995 AC: 4798 AN: 4822

European-Finnish (FIN) AF: 0.990 AC: 10518 AN: 10622

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.970 AC: 65977 AN: 68040

Other (OTH) AF: 0.973 AC: 2058 AN: 2116

Alfa AF: 0.972 Hom.: 9020

Bravo AF: 0.978

Asia WGS AF: 0.996 AC: 3464 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	0.67
DANN	Benign	0.67
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: rs2425897; hg19: chr20-45340892;