20-46724806-AGGAT-A

Position:

• chr20-46724806-AGGAT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_030777.4(SLC2A10):​c.5-196_5-193del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 125,634 control chromosomes in the GnomAD database, including 92 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.031 (92 hom., cov: 26)
• Consequence: SLC2A10 NM_030777.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

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 -10 ACMG points.

• BP6: Variant 20-46724806-AGGAT-A is Benign according to our data. Variant chr20-46724806-AGGAT-A is described in ClinVar as [Benign]. Clinvar id is 1270430.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A10	NM_030777.4	c.5-196_5-193del		intron_variant		ENST00000359271.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A10	ENST00000359271.4	c.5-196_5-193del		intron_variant		1	NM_030777.4	P1
SLC2A10	ENST00000611837.1	n.157-196_157-193del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0306 AC: 3838 AN: 125508 Hom.: 92 Cov.: 26

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0179

Gnomad ASJ AF: 0.0261

Gnomad EAS AF: 0.0197

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0359

Gnomad MID AF: 0.0388

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0306 AC: 3846 AN: 125634 Hom.: 92 Cov.: 26 AF XY: 0.0307 AC XY: 1862 AN XY: 60746

Gnomad4 AFR AF: 0.0692

Gnomad4 AMR AF: 0.0178

Gnomad4 ASJ AF: 0.0261

Gnomad4 EAS AF: 0.0200

Gnomad4 SAS AF: 0.0181

Gnomad4 FIN AF: 0.0359

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0240

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs111504264; hg19: chr20-45353445;