chr4-10021215-G-A

Variant names:

• chr4-10021215-G-A
• rs2276963
• NM_020041.3:c.150+65C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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 -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020041.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_020041.3	MANE Select	c.150+65C>T		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.64-2142C>T		intron	N/A	NP_001001290.1	Q9NRM0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.150+65C>T		intron	N/A	ENSP00000264784.3	Q9NRM0-1
	SLC2A9	ENST00000309065.7	TSL:1	c.64-2142C>T		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.185-2142C>T		intron	N/A

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

African (AFR) AF: 0.179 AC: 5770 AN: 32288

American (AMR) AF: 0.120 AC: 5330 AN: 44554

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 1835 AN: 25756

East Asian (EAS) AF: 0.466 AC: 18349 AN: 39362

South Asian (SAS) AF: 0.143 AC: 12145 AN: 84892

European-Finnish (FIN) AF: 0.0721 AC: 3816 AN: 52890

Middle Eastern (MID) AF: 0.105 AC: 428 AN: 4082

European-Non Finnish (NFE) AF: 0.0356 AC: 37722 AN: 1059288

Other (OTH) AF: 0.0861 AC: 5016 AN: 58252

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

African (AFR) AF: 0.175 AC: 7287 AN: 41542

American (AMR) AF: 0.100 AC: 1533 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3472

East Asian (EAS) AF: 0.460 AC: 2381 AN: 5172

South Asian (SAS) AF: 0.162 AC: 782 AN: 4822

European-Finnish (FIN) AF: 0.0728 AC: 773 AN: 10614

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0367 AC: 2493 AN: 67994

Other (OTH) AF: 0.0951 AC: 201 AN: 2114

Alfa AF: 0.0946 Hom.: 327

Bravo AF: 0.110

Asia WGS AF: 0.276 AC: 956 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.73
PhyloP100		-0.75
PromoterAI		-0.043	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs2276963; hg19: chr4-10022839; COSMIC: COSV53319943; COSMIC: COSV53319943;