chr4-10005651-C-T

Variant names:

• chr4-10005651-C-T
• rs9291642
• NM_020041.3:c.250-8710G>A

Variant summary

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

The NM_020041.3(SLC2A9):​c.250-8710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,236 control chromosomes in the GnomAD database, including 57,877 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 0.87 (57877 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 8 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: AD, AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• hereditary renal hypouricemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.250-8710G>A		intron_variant	Intron 2 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.250-8710G>A		intron_variant	Intron 2 of 11	1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132483 AN: 152118 Hom.: 57826 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.871 AC: 132588 AN: 152236 Hom.: 57877 Cov.: 33 AF XY: 0.870 AC XY: 64788 AN XY: 74428

African (AFR) AF: 0.913 AC: 37920 AN: 41538

American (AMR) AF: 0.816 AC: 12474 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3470

East Asian (EAS) AF: 0.980 AC: 5086 AN: 5190

South Asian (SAS) AF: 0.837 AC: 4032 AN: 4816

European-Finnish (FIN) AF: 0.872 AC: 9231 AN: 10586

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58254 AN: 68022

Other (OTH) AF: 0.860 AC: 1819 AN: 2116

Alfa AF: 0.849 Hom.: 13412

Bravo AF: 0.870

Asia WGS AF: 0.909 AC: 3160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.43
PhyloP100		-0.081
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9291642; hg19: chr4-10007275;