rs13145758

Positions:

• chr4-9980373-G-A
• chr4-9980373-G-C
• chr4-9980373-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_020041.3(SLC2A9):​c.681+219C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 152,076 control chromosomes in the GnomAD database, including 40,346 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.72 (40346 hom., cov: 33)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.287

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 4-9980373-G-A is Benign according to our data. Variant chr4-9980373-G-A is described in ClinVar as [Benign]. Clinvar id is 1261645.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A9	NM_020041.3	c.681+219C>T		intron_variant		ENST00000264784.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A9	ENST00000264784.8	c.681+219C>T		intron_variant		1	NM_020041.3	A2
SLC2A9	ENST00000309065.7	c.594+219C>T		intron_variant		1		P2
SLC2A9	ENST00000505104.5	n.715+219C>T		intron_variant, non_coding_transcript_variant		1
SLC2A9	ENST00000506583.5	c.594+219C>T		intron_variant		5		P2

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109240 AN: 151958 Hom.: 40339 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.719 AC: 109280 AN: 152076 Hom.: 40346 Cov.: 33 AF XY: 0.721 AC XY: 53592 AN XY: 74362

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.741

Alfa AF: 0.713 Hom.: 8136

Bravo AF: 0.699

Asia WGS AF: 0.841 AC: 2924 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.17

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: rs13145758; hg19: chr4-9981997;