chr4-10015763-G-C

Variant names:

• chr4-10015763-G-C
• rs11736479
• NM_020041.3:c.249+3212C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

LOC124900664 (HGNC:):

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020041.3. 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
	SLC2A9	NM_020041.3	MANE Select	c.249+3212C>G		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.162+3212C>G		intron	N/A	NP_001001290.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.249+3212C>G		intron	N/A	ENSP00000264784.3
	SLC2A9	ENST00000309065.7	TSL:1	c.162+3212C>G		intron	N/A	ENSP00000311383.3
	SLC2A9	ENST00000505104.5	TSL:1	n.283+3212C>G		intron	N/A

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

African (AFR) AF: 0.209 AC: 8691 AN: 41524

American (AMR) AF: 0.493 AC: 7532 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1729 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2200 AN: 5164

South Asian (SAS) AF: 0.588 AC: 2840 AN: 4828

European-Finnish (FIN) AF: 0.524 AC: 5541 AN: 10568

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36826 AN: 67980

Other (OTH) AF: 0.458 AC: 969 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11736479; hg19: chr4-10017387;