chr4-9786311-G-A

Position:

• chr4-9786311-G-A

Variant summary

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

The XM_011513856.4(SLC2A9):​c.1420-6246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,710 control chromosomes in the GnomAD database, including 10,216 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 0.36 (10216 hom., cov: 32)
• Consequence: SLC2A9 XM_011513856.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.668

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	XM_006713968.5	c.1601-6246C>T		intron_variant
SLC2A9	XM_011513856.4	c.1420-6246C>T		intron_variant
SLC2A9	XM_011513858.2	c.1333-6246C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000503803.5	n.386-6246C>T		intron_variant, non_coding_transcript_variant		3
SLC2A9	ENST00000508585.5	n.182-14942C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54903 AN: 151590 Hom.: 10197 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.362 AC: 54944 AN: 151710 Hom.: 10216 Cov.: 32 AF XY: 0.364 AC XY: 27008 AN XY: 74122

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.364

Alfa AF: 0.346 Hom.: 1145

Bravo AF: 0.372

Asia WGS AF: 0.421 AC: 1467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2867383; hg19: chr4-9787935;