4-10042008-C-T

Variant names:

• chr4-10042008-C-T
• rs36036984
• ENST00000506583.5:c.-175-1744G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513129.1(SLC2A9):​c.-41+12825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,992 control chromosomes in the GnomAD database, including 1,473 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 0.11 (1473 hom., cov: 33)
• Consequence: SLC2A9 ENST00000513129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-1744G>A		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+12825G>A		intron_variant	Intron 1 of 5	3		ENSP00000426800.1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15927 AN: 151874 Hom.: 1464 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0736

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0374

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.105 AC: 15964 AN: 151992 Hom.: 1473 Cov.: 33 AF XY: 0.111 AC XY: 8245 AN XY: 74306

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.0704

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0736

Gnomad4 NFE AF: 0.0374

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0244 Hom.: 21

Bravo AF: 0.116

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36036984; hg19: chr4-10043632;