4-10042307-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• hypouricemia, renal, 2

  Inheritance: AR, AD, SD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
• hereditary renal hypouricemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

SLC2A9-AS1 (HGNC:59109):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513129.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000506583.5	TSL:5	c.-175-2043C>G		intron	N/A	ENSP00000422209.1	Q9NRM0-2
	SLC2A9	ENST00000513129.1	TSL:3	c.-41+12526C>G		intron	N/A	ENSP00000426800.1	D6REK5
	SLC2A9-AS1	ENST00000733256.1		n.319-13552G>C		intron	N/A

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

African (AFR) AF: 0.359 AC: 14855 AN: 41352

American (AMR) AF: 0.588 AC: 8977 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1968 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4583 AN: 5174

South Asian (SAS) AF: 0.749 AC: 3608 AN: 4820

European-Finnish (FIN) AF: 0.597 AC: 6294 AN: 10536

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 39094 AN: 67950

Other (OTH) AF: 0.550 AC: 1159 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.21
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13124007;

hg19: chr4-10043931;