20-46721941-A-G

Position:

• chr20-46721941-A-G

Variant summary

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

The ENST00000359271.4(SLC2A10):​c.5-3100A>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 152,120 control chromosomes in the GnomAD database, including 7,044 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 (7044 hom., cov: 32)
• Consequence: SLC2A10 ENST00000359271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A10	NM_030777.4	c.5-3100A>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.5-3100A>G		intron_variant		1	NM_030777.4	ENSP00000352216	P1
SLC2A10	ENST00000611837.1	n.157-3100A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42662 AN: 152002 Hom.: 7039 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.281 AC: 42671 AN: 152120 Hom.: 7044 Cov.: 32 AF XY: 0.286 AC XY: 21248 AN XY: 74360

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.326

Alfa AF: 0.310 Hom.: 3549

Bravo AF: 0.281

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
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: rs2425902; hg19: chr20-45350580;