Variant 4-10019133-A-G 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_020041.3(SLC2A9):c.151-60T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,389,166 control chromosomes in the GnomAD database, including 195,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 16337 hom., cov: 34)

Exomes 𝑓: 0.53 ( 178822 hom. )

Consequence

SLC2A9
NM_020041.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.218

Variant links:

Genes affected

SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SLC2A9 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=-0.79).

BP6

Variant 4-10019133-A-G is Benign according to our data. Variant chr4-10019133-A-G is described in ClinVar as [Benign]. Clinvar id is 1286936.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3 link	c.151-60T>C		intron_variant		ENST00000264784.8	NP_064425.2	Q9NRM0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8 link	c.151-60T>C		intron_variant		1	NM_020041.3	ENSP00000264784.3		Q9NRM0-1

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66897

AN:

152052

Hom.:

16328

Cov.:

show subpopulations

Gnomad AFR

AF:

0.208

Gnomad AMI

AF:

0.713

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.498

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.587

Gnomad FIN

AF:

0.525

Gnomad MID

AF:

0.453

Gnomad NFE

AF:

0.541

Gnomad OTH

AF:

0.456

GnomAD4 exome

AF:

0.533

AC:

659487

AN:

1236996

Hom.:

178822

Cov.:

AF XY:

0.536

AC XY:

331109

AN XY:

617602

show subpopulations

Gnomad4 AFR exome

AF:

0.194

Gnomad4 AMR exome

AF:

0.523

Gnomad4 ASJ exome

AF:

0.516

Gnomad4 EAS exome

AF:

0.451

Gnomad4 SAS exome

AF:

0.598

Gnomad4 FIN exome

AF:

0.535

Gnomad4 NFE exome

AF:

0.544

Gnomad4 OTH exome

AF:

0.506

GnomAD4 genome

AF:

0.440

AC:

66915

AN:

152170

Hom.:

16337

Cov.:

AF XY:

0.442

AC XY:

32883

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.208

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.498

Gnomad4 EAS

AF:

0.424

Gnomad4 SAS

AF:

0.588

Gnomad4 FIN

AF:

0.525

Gnomad4 NFE

AF:

0.541

Gnomad4 OTH

AF:

0.457

Alfa

AF:

0.487

Hom.:

3262

Bravo

AF:

0.426

Asia WGS

AF:

0.510

AC:

1769

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.5

DANN

Benign

0.56

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