4-9993558-G-C

Variant names:

• chr4-9993558-G-C
• rs3775948
• NM_020041.3:c.410+3223C>G

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+3223C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,950 control chromosomes in the GnomAD database, including 38,215 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 0.71 (38215 hom., cov: 31)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 72 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.749 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+3223C>G		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.323+3223C>G		intron	N/A	NP_001001290.1
	SLC2A9-AS1	NR_183861.1		n.142+184G>C		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+3223C>G		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.323+3223C>G		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.444+3223C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107421 AN: 151832 Hom.: 38202 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.707 AC: 107474 AN: 151950 Hom.: 38215 Cov.: 31 AF XY: 0.703 AC XY: 52201 AN XY: 74232

African (AFR) AF: 0.662 AC: 27425 AN: 41404

American (AMR) AF: 0.653 AC: 9976 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2317 AN: 3468

East Asian (EAS) AF: 0.585 AC: 3014 AN: 5156

South Asian (SAS) AF: 0.672 AC: 3228 AN: 4800

European-Finnish (FIN) AF: 0.737 AC: 7774 AN: 10554

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51309 AN: 67982

Other (OTH) AF: 0.715 AC: 1509 AN: 2110

Alfa AF: 0.727 Hom.: 19699

Bravo AF: 0.699

Asia WGS AF: 0.669 AC: 2328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		-0.10
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: rs3775948; hg19: chr4-9995182;