4-10015763-G-C

Position:

• chr4-10015763-G-C

Variant summary

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

The NM_020041.3(SLC2A9):​c.249+3212C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,142 control chromosomes in the GnomAD database, including 16,402 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 0.44 (16402 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.249+3212C>G		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.249+3212C>G		intron_variant		1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67091 AN: 152024 Hom.: 16393 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.441 AC: 67109 AN: 152142 Hom.: 16402 Cov.: 33 AF XY: 0.443 AC XY: 32966 AN XY: 74364

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.458

Alfa AF: 0.337 Hom.: 971

Bravo AF: 0.427

Asia WGS AF: 0.510 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.75

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: rs11736479; hg19: chr4-10017387;