chr4-10018856-C-T

Position:

• chr4-10018856-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020041.3(SLC2A9):​c.249+119G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 945,350 control chromosomes in the GnomAD database, including 131,738 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (16386 hom., cov: 33)
  • Exomes 𝑓: 0.54 (115352 hom.)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.224

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 4-10018856-C-T is Benign according to our data. Variant chr4-10018856-C-T is described in ClinVar as [Benign]. Clinvar id is 1226858.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.249+119G>A		intron_variant		ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.249+119G>A		intron_variant		1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66965 AN: 151990 Hom.: 16376 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.448

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.457

GnomAD4 exome AF: 0.535 AC: 424532 AN: 793240 Hom.: 115352 AF XY: 0.539 AC XY: 219041 AN XY: 406482

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.526

Gnomad4 ASJ exome AF: 0.524

Gnomad4 EAS exome AF: 0.461

Gnomad4 SAS exome AF: 0.603

Gnomad4 FIN exome AF: 0.537

Gnomad4 NFE exome AF: 0.547

Gnomad4 OTH exome AF: 0.509

GnomAD4 genome AF: 0.440 AC: 66984 AN: 152110 Hom.: 16386 Cov.: 33 AF XY: 0.443 AC XY: 32909 AN XY: 74354

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.457

Alfa AF: 0.476 Hom.: 2312

Bravo AF: 0.426

Asia WGS AF: 0.513 AC: 1781 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-0.79
CADD	Benign	6.4
DANN	Benign	0.79
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: rs2240720; hg19: chr4-10020480;