4-10040938-A-T

Variant names:

• chr4-10040938-A-T
• rs7349721
• ENST00000506583.5:c.-175-674T>A

Variant summary

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

The ENST00000506583.5(SLC2A9):​c.-175-674T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,160 control chromosomes in the GnomAD database, including 45,643 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 0.77 (45643 hom., cov: 32)
• Consequence: SLC2A9 ENST00000506583.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000506583.5	c.-175-674T>A		intron_variant	Intron 1 of 13	5		ENSP00000422209.1
SLC2A9	ENST00000513129.1	c.-41+13895T>A		intron_variant	Intron 1 of 5	3		ENSP00000426800.1
SLC2A9-AS1	ENST00000733256.1	n.319-14921A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117078 AN: 152042 Hom.: 45612 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.770 AC: 117153 AN: 152160 Hom.: 45643 Cov.: 32 AF XY: 0.764 AC XY: 56841 AN XY: 74400

African (AFR) AF: 0.780 AC: 32393 AN: 41510

American (AMR) AF: 0.632 AC: 9666 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2472 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2679 AN: 5164

South Asian (SAS) AF: 0.678 AC: 3268 AN: 4820

European-Finnish (FIN) AF: 0.798 AC: 8453 AN: 10592

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55650 AN: 68000

Other (OTH) AF: 0.760 AC: 1607 AN: 2114

Alfa AF: 0.793 Hom.: 5633

Bravo AF: 0.758

Asia WGS AF: 0.643 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.5
DANN	Benign	0.76
PhyloP100		0.087
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7349721; hg19: chr4-10042562;