20-46720078-T-C

Variant names:

• chr20-46720078-T-C
• rs2143044
• NM_030777.4:c.5-4963T>C

Variant summary

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

The NM_030777.4(SLC2A10):​c.5-4963T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,042 control chromosomes in the GnomAD database, including 18,415 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 0.48 (18415 hom., cov: 32)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A10	NM_030777.4	c.5-4963T>C		intron_variant	Intron 1 of 4	ENST00000359271.4	NP_110404.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A10	ENST00000359271.4	c.5-4963T>C		intron_variant	Intron 1 of 4	1	NM_030777.4	ENSP00000352216.2
SLC2A10	ENST00000611837.1	n.157-4963T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72727 AN: 151924 Hom.: 18364 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.479 AC: 72833 AN: 152042 Hom.: 18415 Cov.: 32 AF XY: 0.485 AC XY: 36016 AN XY: 74312

African (AFR) AF: 0.613 AC: 25413 AN: 41452

American (AMR) AF: 0.562 AC: 8586 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1513 AN: 3470

East Asian (EAS) AF: 0.689 AC: 3561 AN: 5166

South Asian (SAS) AF: 0.513 AC: 2471 AN: 4814

European-Finnish (FIN) AF: 0.420 AC: 4442 AN: 10578

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25424 AN: 67954

Other (OTH) AF: 0.482 AC: 1019 AN: 2112

Alfa AF: 0.401 Hom.: 6376

Bravo AF: 0.495

Asia WGS AF: 0.598 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2143044; hg19: chr20-45348717;