4-10021215-G-A

Position:

• chr4-10021215-G-A

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.150+65C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0683 in 1,553,604 control chromosomes in the GnomAD database, including 8,868 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.10 (1428 hom., cov: 33)
  • Exomes 𝑓: 0.065 (7440 hom.)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.753

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=-0.85).
• BP6: Variant 4-10021215-G-A is Benign according to our data. Variant chr4-10021215-G-A is described in ClinVar as [Benign]. Clinvar id is 1182363.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.150+65C>T		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.150+65C>T		intron_variant		1	NM_020041.3	ENSP00000264784	A2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15704 AN: 152122 Hom.: 1414 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0728

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0908

GnomAD4 exome AF: 0.0645 AC: 90411 AN: 1401364 Hom.: 7440 AF XY: 0.0661 AC XY: 46315 AN XY: 700338

Gnomad4 AFR exome AF: 0.179

Gnomad4 AMR exome AF: 0.120

Gnomad4 ASJ exome AF: 0.0712

Gnomad4 EAS exome AF: 0.466

Gnomad4 SAS exome AF: 0.143

Gnomad4 FIN exome AF: 0.0721

Gnomad4 NFE exome AF: 0.0356

Gnomad4 OTH exome AF: 0.0861

GnomAD4 genome AF: 0.103 AC: 15754 AN: 152240 Hom.: 1428 Cov.: 33 AF XY: 0.108 AC XY: 8003 AN XY: 74442

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0728

Gnomad4 NFE AF: 0.0367

Gnomad4 OTH AF: 0.0951

Alfa AF: 0.0455 Hom.: 65

Bravo AF: 0.110

Asia WGS AF: 0.276 AC: 956 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	-0.85
CADD	Benign	1.4
DANN	Benign	0.73
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2276963; hg19: chr4-10022839; COSMIC: COSV53319943; COSMIC: COSV53319943;