Variant 20-46729584-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_030777.4(SLC2A10):c.1547+96C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 1,313,316 control chromosomes in the GnomAD database, including 126,068 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.38 ( 11408 hom., cov: 27)

Exomes 𝑓: 0.45 ( 114660 hom. )

Consequence

SLC2A10
NM_030777.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.113

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 20-46729584-C-T is Benign according to our data. Variant chr20-46729584-C-T is described in ClinVar as [Benign]. Clinvar id is 673813.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A10	NM_030777.4 linkuse as main transcript	c.1547+96C>T		intron_variant		ENST00000359271.4	NP_110404.1	O95528

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A10	ENST00000359271.4 linkuse as main transcript	c.1547+96C>T		intron_variant		1	NM_030777.4	ENSP00000352216.2		O95528

Frequencies

GnomAD3 genomes

AF:

0.383

AC:

55843

AN:

145736

Hom.:

11399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.224

Gnomad AMI

AF:

0.365

Gnomad AMR

AF:

0.457

Gnomad ASJ

AF:

0.429

Gnomad EAS

AF:

0.615

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.489

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.428

Gnomad OTH

AF:

0.415

GnomAD4 exome

AF:

0.453

AC:

528404

AN:

1167498

Hom.:

114660

AF XY:

0.449

AC XY:

264784

AN XY:

589408

show subpopulations

Gnomad4 AFR exome

AF:

0.240

Gnomad4 AMR exome

AF:

0.439

Gnomad4 ASJ exome

AF:

0.482

Gnomad4 EAS exome

AF:

0.651

Gnomad4 SAS exome

AF:

0.355

Gnomad4 FIN exome

AF:

0.493

Gnomad4 NFE exome

AF:

0.458

Gnomad4 OTH exome

AF:

0.461

GnomAD4 genome

AF:

0.383

AC:

55874

AN:

145818

Hom.:

11408

Cov.:

AF XY:

0.389

AC XY:

27421

AN XY:

70552

show subpopulations

Gnomad4 AFR

AF:

0.224

Gnomad4 AMR

AF:

0.456

Gnomad4 ASJ

AF:

0.429

Gnomad4 EAS

AF:

0.614

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.489

Gnomad4 NFE

AF:

0.428

Gnomad4 OTH

AF:

0.417

Alfa

AF:

0.416

Hom.:

22182

Bravo

AF:

0.370

Asia WGS

AF:

0.426

AC:

1479

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.90

DANN

Benign

0.62

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over