rs13145758

Variant names:

• chr4-9980373-G-A
• rs13145758
• NM_020041.3:c.681+219C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-9980373-G-A
• chr4-9980373-G-C
• chr4-9980373-G-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_020041.3(SLC2A9):​c.681+219C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,076 control chromosomes in the GnomAD database, including 40,346 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.72 (40346 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.287
• Publications: 7 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 4-9980373-G-A is Benign according to our data. Variant chr4-9980373-G-A is described in ClinVar as [Benign]. Clinvar id is 1261645.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.681+219C>T		intron_variant	Intron 5 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.681+219C>T		intron_variant	Intron 5 of 11	1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109240 AN: 151958 Hom.: 40339 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.719 AC: 109280 AN: 152076 Hom.: 40346 Cov.: 33 AF XY: 0.721 AC XY: 53592 AN XY: 74362

African (AFR) AF: 0.551 AC: 22797 AN: 41402

American (AMR) AF: 0.645 AC: 9861 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2546 AN: 3472

East Asian (EAS) AF: 0.981 AC: 5097 AN: 5194

South Asian (SAS) AF: 0.774 AC: 3732 AN: 4822

European-Finnish (FIN) AF: 0.827 AC: 8751 AN: 10580

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53927 AN: 68016

Other (OTH) AF: 0.741 AC: 1560 AN: 2106

Alfa AF: 0.707 Hom.: 9348

Bravo AF: 0.699

Asia WGS AF: 0.841 AC: 2924 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.17
PhyloP100		-0.29
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: rs13145758; hg19: chr4-9981997;