rs13113918

Variant names:

• chr4-9996869-A-G
• rs13113918
• NM_020041.3:c.322T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-9996869-A-G
• chr4-9996869-A-C
• chr4-9996869-A-T

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_020041.3(SLC2A9):​c.322T>C​(p.Leu108Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 1,613,808 control chromosomes in the GnomAD database, including 509,519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.79 (47368 hom., cov: 33)
  • Exomes 𝑓: 0.79 (462151 hom.)
• Consequence: SLC2A9 NM_020041.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 1.96
• Publications: 34 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-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BP6: Variant 4-9996869-A-G is Benign according to our data. Variant chr4-9996869-A-G is described in ClinVar as Benign. ClinVar VariationId is 350240.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=1.96 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020041.3. 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
	SLC2A9	NM_020041.3	MANE Select	c.322T>C	p.Leu108Leu	synonymous	Exon 3 of 12	NP_064425.2
	SLC2A9	NM_001001290.2		c.235T>C	p.Leu79Leu	synonymous	Exon 4 of 13	NP_001001290.1	Q9NRM0-2
	SLC2A9-AS1	NR_183861.1		n.308-2224A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.322T>C	p.Leu108Leu	synonymous	Exon 3 of 12	ENSP00000264784.3	Q9NRM0-1
	SLC2A9	ENST00000309065.7	TSL:1	c.235T>C	p.Leu79Leu	synonymous	Exon 4 of 13	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.356T>C		non_coding_transcript_exon	Exon 4 of 12

Frequencies

GnomAD3 genomes AF: 0.788 AC: 119841 AN: 152120 Hom.: 47343 Cov.: 33

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.785

GnomAD2 exomes AF: 0.798 AC: 200740 AN: 251422 AF XY: 0.797

Gnomad AFR exome AF: 0.772

Gnomad AMR exome AF: 0.769

Gnomad ASJ exome AF: 0.733

Gnomad EAS exome AF: 0.980

Gnomad FIN exome AF: 0.793

Gnomad NFE exome AF: 0.791

Gnomad OTH exome AF: 0.789

GnomAD4 exome AF: 0.794 AC: 1160636 AN: 1461570 Hom.: 462151 Cov.: 49 AF XY: 0.794 AC XY: 576996 AN XY: 727118

African (AFR) AF: 0.776 AC: 25993 AN: 33476

American (AMR) AF: 0.768 AC: 34363 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 19274 AN: 26132

East Asian (EAS) AF: 0.985 AC: 39113 AN: 39698

South Asian (SAS) AF: 0.788 AC: 68004 AN: 86254

European-Finnish (FIN) AF: 0.797 AC: 42583 AN: 53412

Middle Eastern (MID) AF: 0.758 AC: 4373 AN: 5768

European-Non Finnish (NFE) AF: 0.791 AC: 879012 AN: 1111734

Other (OTH) AF: 0.794 AC: 47921 AN: 60374

GnomAD4 genome AF: 0.788 AC: 119918 AN: 152238 Hom.: 47368 Cov.: 33 AF XY: 0.788 AC XY: 58653 AN XY: 74424

African (AFR) AF: 0.777 AC: 32263 AN: 41524

American (AMR) AF: 0.747 AC: 11440 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2518 AN: 3472

East Asian (EAS) AF: 0.977 AC: 5047 AN: 5168

South Asian (SAS) AF: 0.790 AC: 3818 AN: 4830

European-Finnish (FIN) AF: 0.795 AC: 8426 AN: 10604

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53768 AN: 68018

Other (OTH) AF: 0.787 AC: 1663 AN: 2112

Alfa AF: 0.784 Hom.: 78739

Bravo AF: 0.786

Asia WGS AF: 0.883 AC: 3069 AN: 3478

EpiCase AF: 0.784

EpiControl AF: 0.779

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	3	not provided (3)
-	-	2	Hypouricemia, renal, 2 (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		2.0
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: rs13113918; hg19: chr4-9998493; COSMIC: COSV108066860;