4-10042064-C-T

Variant names:

• chr4-10042064-C-T
• rs6850166
• ENST00000506583.5:c.-175-1800G>A

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-175-1800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,932 control chromosomes in the GnomAD database, including 10,224 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 0.34 (10224 hom., cov: 32)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506583.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000506583.5	TSL:5	c.-175-1800G>A		intron	N/A	ENSP00000422209.1
	SLC2A9	ENST00000513129.1	TSL:3	c.-41+12769G>A		intron	N/A	ENSP00000426800.1
	SLC2A9-AS1	ENST00000733256.1		n.319-13795C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50966 AN: 151814 Hom.: 10201 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.0921

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.336 AC: 51019 AN: 151932 Hom.: 10224 Cov.: 32 AF XY: 0.329 AC XY: 24419 AN XY: 74240

African (AFR) AF: 0.556 AC: 23028 AN: 41398

American (AMR) AF: 0.229 AC: 3493 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3464

East Asian (EAS) AF: 0.0935 AC: 483 AN: 5168

South Asian (SAS) AF: 0.0912 AC: 439 AN: 4816

European-Finnish (FIN) AF: 0.276 AC: 2906 AN: 10520

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19063 AN: 67968

Other (OTH) AF: 0.311 AC: 655 AN: 2108

Alfa AF: 0.324 Hom.: 1095

Bravo AF: 0.344

Asia WGS AF: 0.131 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	12
DANN	Benign	0.90
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6850166; hg19: chr4-10043688;