chr4-10041291-T-A

Variant names:

• chr4-10041291-T-A
• rs13101785
• ENST00000506583.5:c.-175-1027A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513129.1(SLC2A9):​c.-41+13542A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,142 control chromosomes in the GnomAD database, including 15,605 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 0.43 (15605 hom., cov: 33)
• Consequence: SLC2A9 ENST00000513129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 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.-175-1027A>T		intron	N/A	ENSP00000422209.1	Q9NRM0-2
	SLC2A9	ENST00000513129.1	TSL:3	c.-41+13542A>T		intron	N/A	ENSP00000426800.1	D6REK5
	SLC2A9-AS1	ENST00000733256.1		n.319-14568T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65284 AN: 152024 Hom.: 15601 Cov.: 33

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.429 AC: 65297 AN: 152142 Hom.: 15605 Cov.: 33 AF XY: 0.430 AC XY: 31981 AN XY: 74366

African (AFR) AF: 0.208 AC: 8622 AN: 41530

American (AMR) AF: 0.401 AC: 6135 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3472

East Asian (EAS) AF: 0.426 AC: 2198 AN: 5164

South Asian (SAS) AF: 0.587 AC: 2834 AN: 4826

European-Finnish (FIN) AF: 0.523 AC: 5517 AN: 10554

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36568 AN: 67994

Other (OTH) AF: 0.445 AC: 940 AN: 2114

Alfa AF: 0.469 Hom.: 2235

Bravo AF: 0.409

Asia WGS AF: 0.509 AC: 1768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.77
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13101785; hg19: chr4-10042915;