4-10022679-T-C

Position:

• chr4-10022679-T-C

Variant summary

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

The ENST00000309065.7(SLC2A9):​c.63+3225A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,090 control chromosomes in the GnomAD database, including 41,708 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 0.73 (41708 hom., cov: 33)
• Consequence: SLC2A9 ENST00000309065.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_001001290.2	c.63+3225A>G		intron_variant
SLC2A9	XM_011513858.2	c.63+3225A>G		intron_variant
SLC2A9	XM_047415973.1	c.63+3225A>G		intron_variant
SLC2A9	XM_047415975.1	c.63+3225A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000309065.7	c.63+3225A>G		intron_variant		1		P2
SLC2A9	ENST00000505104.5	n.184+3225A>G		intron_variant, non_coding_transcript_variant		1
SLC2A9	ENST00000506583.5	c.63+3225A>G		intron_variant		5		P2
SLC2A9	ENST00000513129.1	c.63+3225A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111562 AN: 151970 Hom.: 41676 Cov.: 33

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.734 AC: 111645 AN: 152090 Hom.: 41708 Cov.: 33 AF XY: 0.737 AC XY: 54779 AN XY: 74370

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.732

Alfa AF: 0.768 Hom.: 41384

Bravo AF: 0.720

Asia WGS AF: 0.883 AC: 3067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12509955; hg19: chr4-10024303;