rs1878275

Variant names:

• chr4-9775777-A-C
• rs1878275
• XM_006713968.5:c.*4197T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-9775777-A-C
• chr4-9775777-A-G
• chr4-9775777-A-T

Variant summary

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

The XM_006713968.5(SLC2A9):​c.*4197T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,200 control chromosomes in the GnomAD database, including 67,275 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 0.94 (67275 hom., cov: 31)
• Consequence: SLC2A9 XM_006713968.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	XM_006713968.5	c.*4197T>G		3_prime_UTR_variant	Exon 13 of 13		XP_006714031.1
SLC2A9	XM_047415974.1	c.*4046T>G		3_prime_UTR_variant	Exon 12 of 12		XP_047271930.1
SLC2A9	XM_047415977.1	c.*4197T>G		3_prime_UTR_variant	Exon 12 of 12		XP_047271933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000508585.5	n.182-4408T>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142808 AN: 152082 Hom.: 67208 Cov.: 31

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.939 AC: 142933 AN: 152200 Hom.: 67275 Cov.: 31 AF XY: 0.936 AC XY: 69674 AN XY: 74406

African (AFR) AF: 0.948 AC: 39334 AN: 41486

American (AMR) AF: 0.898 AC: 13734 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3269 AN: 3472

East Asian (EAS) AF: 0.811 AC: 4186 AN: 5164

South Asian (SAS) AF: 0.841 AC: 4053 AN: 4820

European-Finnish (FIN) AF: 0.964 AC: 10230 AN: 10610

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.955 AC: 64952 AN: 68028

Other (OTH) AF: 0.947 AC: 2001 AN: 2114

Alfa AF: 0.944 Hom.: 8772

Bravo AF: 0.935

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.70
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1878275; hg19: chr4-9777401;