4-9775777-A-C

Position:

• chr4-9775777-A-C

Variant summary

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

The XM_006713968.5(SLC2A9):​c.*4197T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,200 control chromosomes in the GnomAD database, including 67,275 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 0.94 (67275 hom., cov: 31)
• Consequence: SLC2A9 XM_006713968.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	XM_006713968.5	c.*4197T>G		3_prime_UTR_variant	13/13		XP_006714031.1
SLC2A9	XM_047415974.1	c.*4046T>G		3_prime_UTR_variant	12/12		XP_047271930.1
SLC2A9	XM_047415977.1	c.*4197T>G		3_prime_UTR_variant	12/12		XP_047271933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000508585.5	n.182-4408T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142808 AN: 152082 Hom.: 67208 Cov.: 31

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.939 AC: 142933 AN: 152200 Hom.: 67275 Cov.: 31 AF XY: 0.936 AC XY: 69674 AN XY: 74406

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.947

Alfa AF: 0.943 Hom.: 8427

Bravo AF: 0.935

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878275; hg19: chr4-9777401;