4-9995679-G-A

Variant names:

• chr4-9995679-G-A
• rs3733588
• NM_020041.3:c.410+1102C>T

Variant summary

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

The NM_020041.3(SLC2A9):​c.410+1102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,088 control chromosomes in the GnomAD database, including 39,243 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 0.72 (39238 hom., cov: 32)
  • Exomes 𝑓: 1.0 (5 hom.)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 11 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_020041.3	MANE Select	c.410+1102C>T		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.323+1102C>T		intron	N/A	NP_001001290.1
	SLC2A9-AS1	NR_183861.1		n.307+1154G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.410+1102C>T		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.323+1102C>T		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.444+1102C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108897 AN: 151960 Hom.: 39222 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.725

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 Cov.: 0 AF XY: 1.00 AC XY: 6 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 6 AN: 6

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.716 AC: 108955 AN: 152078 Hom.: 39238 Cov.: 32 AF XY: 0.712 AC XY: 52928 AN XY: 74334

African (AFR) AF: 0.688 AC: 28520 AN: 41452

American (AMR) AF: 0.662 AC: 10116 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2328 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3027 AN: 5174

South Asian (SAS) AF: 0.679 AC: 3262 AN: 4806

European-Finnish (FIN) AF: 0.735 AC: 7774 AN: 10574

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51478 AN: 67998

Other (OTH) AF: 0.724 AC: 1527 AN: 2110

Alfa AF: 0.710 Hom.: 12479

Bravo AF: 0.710

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.79
DANN	Benign	0.67
PhyloP100		-0.41
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: rs3733588; hg19: chr4-9997303;