NM_030777.4:c.5-3584A>T

Variant names:

• chr20-46721457-A-T
• rs3092412
• NM_030777.4:c.5-3584A>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.5-3584A>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 150,036 control chromosomes in the GnomAD database, including 6,912 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 (6912 hom., cov: 31)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 4 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, Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, G2P
• familial thoracic aortic aneurysm and aortic dissection

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A10	NM_030777.4	MANE Select	c.5-3584A>T		intron	N/A	NP_110404.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A10	ENST00000359271.4	TSL:1 MANE Select	c.5-3584A>T		intron	N/A	ENSP00000352216.2
	SLC2A10	ENST00000611837.1	TSL:2	n.157-3584A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42215 AN: 149960 Hom.: 6907 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.314

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.281 AC: 42216 AN: 150036 Hom.: 6912 Cov.: 31 AF XY: 0.286 AC XY: 20939 AN XY: 73140

African (AFR) AF: 0.113 AC: 4640 AN: 41054

American (AMR) AF: 0.386 AC: 5821 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1310 AN: 3458

East Asian (EAS) AF: 0.578 AC: 2950 AN: 5102

South Asian (SAS) AF: 0.301 AC: 1427 AN: 4736

European-Finnish (FIN) AF: 0.317 AC: 3116 AN: 9838

Middle Eastern (MID) AF: 0.326 AC: 94 AN: 288

European-Non Finnish (NFE) AF: 0.325 AC: 21941 AN: 67492

Other (OTH) AF: 0.327 AC: 677 AN: 2070

Alfa AF: 0.267 Hom.: 758

Bravo AF: 0.283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.44
PhyloP100		-0.36
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: rs3092412; hg19: chr20-45350096;