4-10005039-G-T

Variant names:

• chr4-10005039-G-T
• rs10016075
• NM_020041.3:c.250-8098C>A

Variant summary

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

The NM_020041.3(SLC2A9):​c.250-8098C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,062 control chromosomes in the GnomAD database, including 40,789 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 0.73 (40789 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 5 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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 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.250-8098C>A		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.163-8098C>A		intron	N/A	NP_001001290.1
	SLC2A9-AS1	NR_183861.1		n.*140G>T		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.250-8098C>A		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.163-8098C>A		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.284-8098C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110308 AN: 151942 Hom.: 40778 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.726 AC: 110356 AN: 152062 Hom.: 40789 Cov.: 32 AF XY: 0.722 AC XY: 53677 AN XY: 74336

African (AFR) AF: 0.618 AC: 25627 AN: 41440

American (AMR) AF: 0.697 AC: 10660 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2477 AN: 3472

East Asian (EAS) AF: 0.511 AC: 2637 AN: 5156

South Asian (SAS) AF: 0.660 AC: 3178 AN: 4816

European-Finnish (FIN) AF: 0.789 AC: 8332 AN: 10564

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54970 AN: 68002

Other (OTH) AF: 0.730 AC: 1541 AN: 2112

Alfa AF: 0.753 Hom.: 25981

Bravo AF: 0.715

Asia WGS AF: 0.615 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.4
DANN	Benign	0.88
PhyloP100		0.21
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: rs10016075; hg19: chr4-10006663;