Variant rs938554 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020041.3(SLC2A9):c.815-3496G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,958 control chromosomes in the GnomAD database, including 40,028 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 0.72 ( 39998 hom., cov: 30)

Exomes 𝑓: 0.77 ( 30 hom. )

Consequence

SLC2A9
NM_020041.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.221

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:

ENSG00000249219 (HGNC:):

ENSG00000249219 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3 link	c.815-3496G>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.815-3496G>C		intron_variant		1	NM_020041.3	ENSP00000264784.3		Q9NRM0-1

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

108918

AN:

151736

Hom.:

39974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.572

Gnomad AMI

AF:

0.836

Gnomad AMR

AF:

0.639

Gnomad ASJ

AF:

0.750

Gnomad EAS

AF:

0.981

Gnomad SAS

AF:

0.771

Gnomad FIN

AF:

0.818

Gnomad MID

AF:

0.736

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.732

GnomAD4 exome

AF:

0.775

AC:

AN:

102

Hom.:

Cov.:

AF XY:

0.762

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.813

Gnomad4 OTH exome

AF:

0.750

GnomAD4 genome

AF:

0.718

AC:

108991

AN:

151856

Hom.:

39998

Cov.:

AF XY:

0.720

AC XY:

53458

AN XY:

74204

show subpopulations

Gnomad4 AFR

AF:

0.573

Gnomad4 AMR

AF:

0.638

Gnomad4 ASJ

AF:

0.750

Gnomad4 EAS

AF:

0.981

Gnomad4 SAS

AF:

0.770

Gnomad4 FIN

AF:

0.818

Gnomad4 NFE

AF:

0.781

Gnomad4 OTH

AF:

0.735

Alfa

AF:

0.748

Hom.:

5357

Bravo

AF:

0.700

Asia WGS

AF:

0.847

AC:

2947

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.83

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over