20-46724806-A-AGGAT

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_5-193dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0785 in 125,594 control chromosomes in the GnomAD database, including 428 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.079 (428 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-A-AGGAT is Benign according to our data. Variant chr20-46724806-A-AGGAT is described in ClinVar as [Benign]. Clinvar id is 1283392.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0784 AC: 9840 AN: 125468 Hom.: 424 Cov.: 26

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.0104

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0542

Gnomad MID AF: 0.0340

Gnomad NFE AF: 0.0773

Gnomad OTH AF: 0.0600

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

GnomAD4 genome AF: 0.0785 AC: 9861 AN: 125594 Hom.: 428 Cov.: 26 AF XY: 0.0760 AC XY: 4615 AN XY: 60722

Gnomad4 AFR AF: 0.0903

Gnomad4 AMR AF: 0.0586

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.0719

Gnomad4 FIN AF: 0.0542

Gnomad4 NFE AF: 0.0773

Gnomad4 OTH AF: 0.0626

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

Nov 14, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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;