4-10042307-G-C

Variant names:

• chr4-10042307-G-C
• rs13124007
• ENST00000506583.5:c.-175-2043C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513129.1(SLC2A9):​c.-41+12526C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,892 control chromosomes in the GnomAD database, including 23,006 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 0.54 (23006 hom., cov: 32)
• Consequence: SLC2A9 ENST00000513129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-2043C>G		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+12526C>G		intron_variant	Intron 1 of 5	3		ENSP00000426800.1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81328 AN: 151774 Hom.: 22990 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.536 AC: 81380 AN: 151892 Hom.: 23006 Cov.: 32 AF XY: 0.543 AC XY: 40277 AN XY: 74232

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.550

Alfa AF: 0.530 Hom.: 2667

Bravo AF: 0.526

Asia WGS AF: 0.782 AC: 2715 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	0.44
DANN	Benign	0.21

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13124007; hg19: chr4-10043931;