rs874432

chr4-9918982-T-A

Variant summary

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

The NM_020041.3(SLC2A9):c.1002+1403A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,984 control chromosomes in the GnomAD database, including 7,045 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 0.28 (7045 hom., cov: 32)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.1002+1403A>T		intron_variant		ENST00000264784.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.1002+1403A>T		intron_variant		1	NM_020041.3	A2
SLC2A9	ENST00000309065.7	c.915+1403A>T		intron_variant		1		P2
SLC2A9	ENST00000505104.5	n.1036+1403A>T		intron_variant, non_coding_transcript_variant		1
SLC2A9	ENST00000506583.5	c.915+1403A>T		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43205 AN: 151866 Hom.: 7034 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.285 AC: 43253 AN: 151984 Hom.: 7045 Cov.: 32 AF XY: 0.282 AC XY: 20910 AN XY: 74278

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.271

Alfa AF: 0.256 Hom.: 692

Bravo AF: 0.302

Asia WGS AF: 0.153 AC: 531 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	2.1
Dann	Benign	0.60

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: rs874432; hg19: chr4-9920606;