chr20-46731580-C-G

Position:

• chr20-46731580-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000359271.4(SLC2A10):​c.1547+2092C>G 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 151,970 control chromosomes in the GnomAD database, including 7,063 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 (7063 hom., cov: 31)
• Consequence: SLC2A10 ENST00000359271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A10	NM_030777.4	c.1547+2092C>G		intron_variant		ENST00000359271.4	NP_110404.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A10	ENST00000359271.4	c.1547+2092C>G		intron_variant		1	NM_030777.4	ENSP00000352216	P1

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42702 AN: 151852 Hom.: 7057 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.281 AC: 42712 AN: 151970 Hom.: 7063 Cov.: 31 AF XY: 0.286 AC XY: 21258 AN XY: 74234

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.328

Alfa AF: 0.170 Hom.: 370

Bravo AF: 0.282

Asia WGS AF: 0.394 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.7
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2425911; hg19: chr20-45360219;