4-9992214-C-T

Variant names:

• chr4-9992214-C-T
• rs7663032
• NM_020041.3:c.410+4567G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020041.3(SLC2A9):​c.410+4567G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,014 control chromosomes in the GnomAD database, including 37,979 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 0.70 (37979 hom., cov: 31)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 8 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]

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.410+4567G>A		intron_variant	Intron 3 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.410+4567G>A		intron_variant	Intron 3 of 11	1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106990 AN: 151896 Hom.: 37962 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.704 AC: 107047 AN: 152014 Hom.: 37979 Cov.: 31 AF XY: 0.699 AC XY: 51932 AN XY: 74288

African (AFR) AF: 0.662 AC: 27420 AN: 41442

American (AMR) AF: 0.651 AC: 9950 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2263 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2616 AN: 5156

South Asian (SAS) AF: 0.636 AC: 3056 AN: 4802

European-Finnish (FIN) AF: 0.737 AC: 7780 AN: 10560

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51555 AN: 67988

Other (OTH) AF: 0.707 AC: 1492 AN: 2110

Alfa AF: 0.673 Hom.: 6553

Bravo AF: 0.697

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.40
PhyloP100		1.5
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: rs7663032; hg19: chr4-9993838;