20-46721457-A-T

Position:

• chr20-46721457-A-T

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A10	NM_030777.4	c.5-3584A>T		intron_variant		ENST00000359271.4	NP_110404.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A10	ENST00000359271.4	c.5-3584A>T		intron_variant		1	NM_030777.4	ENSP00000352216.2
SLC2A10	ENST00000611837.1	n.157-3584A>T		intron_variant		2

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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.327

Alfa AF: 0.267 Hom.: 758

Bravo AF: 0.283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
DANN	Benign	0.44

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

Publications

LitVar

Other links and lift over

dbSNP: rs3092412; hg19: chr20-45350096;