NM_020041.3:c.249+7426A>C

Variant names:

• chr4-10011549-T-G
• rs6845554
• NM_020041.3:c.249+7426A>C

Variant summary

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

The NM_020041.3(SLC2A9):​c.249+7426A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,172 control chromosomes in the GnomAD database, including 24,211 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 0.56 (24211 hom., cov: 34)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 10 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]

LOC124900664 (HGNC:):

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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.249+7426A>C		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.162+7426A>C		intron	N/A	NP_001001290.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.249+7426A>C		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.162+7426A>C		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.283+7426A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84385 AN: 152054 Hom.: 24180 Cov.: 34

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.555 AC: 84463 AN: 152172 Hom.: 24211 Cov.: 34 AF XY: 0.562 AC XY: 41781 AN XY: 74378

African (AFR) AF: 0.420 AC: 17458 AN: 41518

American (AMR) AF: 0.596 AC: 9126 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1973 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4595 AN: 5182

South Asian (SAS) AF: 0.750 AC: 3617 AN: 4820

European-Finnish (FIN) AF: 0.598 AC: 6323 AN: 10580

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39347 AN: 67986

Other (OTH) AF: 0.561 AC: 1182 AN: 2108

Alfa AF: 0.578 Hom.: 13195

Bravo AF: 0.549

Asia WGS AF: 0.789 AC: 2740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.39
PhyloP100		-1.1
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: rs6845554; hg19: chr4-10013173;