4-9933120-G-T

Position:

• chr4-9933120-G-T

Variant summary

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

The NM_020041.3(SLC2A9):​c.814+8793C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,106 control chromosomes in the GnomAD database, including 9,508 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 0.33 (9508 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.814+8793C>A		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.814+8793C>A		intron_variant		1	NM_020041.3	ENSP00000264784.3
SLC2A9	ENST00000309065.7	c.727+8793C>A		intron_variant		1		ENSP00000311383.3
SLC2A9	ENST00000505104.5	n.848+8793C>A		intron_variant		1
SLC2A9	ENST00000506583.5	c.727+8793C>A		intron_variant		5		ENSP00000422209.1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49714 AN: 151988 Hom.: 9475 Cov.: 33

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.327 AC: 49805 AN: 152106 Hom.: 9508 Cov.: 33 AF XY: 0.325 AC XY: 24164 AN XY: 74384

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0204

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.309

Alfa AF: 0.256 Hom.: 11893

Bravo AF: 0.347

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
DANN	Benign	0.38

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

Publications

LitVar

Other links and lift over

dbSNP: rs737267; hg19: chr4-9934744;