rs2240722

Variant names:

• chr4-10019133-A-G
• rs2240722
• NM_020041.3:c.151-60T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-10019133-A-G
• chr4-10019133-A-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.151-60T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,389,166 control chromosomes in the GnomAD database, including 195,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.44 (16337 hom., cov: 34)
  • Exomes 𝑓: 0.53 (178822 hom.)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.218
• Publications: 12 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=-0.79).
• BP6: Variant 4-10019133-A-G is Benign according to our data. Variant chr4-10019133-A-G is described in ClinVar as Benign. ClinVar VariationId is 1286936.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 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.151-60T>C		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.64-60T>C		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.151-60T>C		intron	N/A	ENSP00000264784.3	Q9NRM0-1
	SLC2A9	ENST00000309065.7	TSL:1	c.64-60T>C		intron	N/A	ENSP00000311383.3	Q9NRM0-2
	SLC2A9	ENST00000505104.5	TSL:1	n.185-60T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66897 AN: 152052 Hom.: 16328 Cov.: 34

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.456

GnomAD4 exome AF: 0.533 AC: 659487 AN: 1236996 Hom.: 178822 Cov.: 18 AF XY: 0.536 AC XY: 331109 AN XY: 617602

African (AFR) AF: 0.194 AC: 5494 AN: 28336

American (AMR) AF: 0.523 AC: 18516 AN: 35388

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 12456 AN: 24124

East Asian (EAS) AF: 0.451 AC: 15754 AN: 34968

South Asian (SAS) AF: 0.598 AC: 45422 AN: 76014

European-Finnish (FIN) AF: 0.535 AC: 25992 AN: 48610

Middle Eastern (MID) AF: 0.463 AC: 2410 AN: 5208

European-Non Finnish (NFE) AF: 0.544 AC: 506768 AN: 931644

Other (OTH) AF: 0.506 AC: 26675 AN: 52704

GnomAD4 genome AF: 0.440 AC: 66915 AN: 152170 Hom.: 16337 Cov.: 34 AF XY: 0.442 AC XY: 32883 AN XY: 74382

African (AFR) AF: 0.208 AC: 8630 AN: 41548

American (AMR) AF: 0.489 AC: 7485 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1729 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2184 AN: 5146

South Asian (SAS) AF: 0.588 AC: 2839 AN: 4832

European-Finnish (FIN) AF: 0.525 AC: 5561 AN: 10588

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36741 AN: 67974

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.464 Hom.: 3625

Bravo AF: 0.426

Asia WGS AF: 0.510 AC: 1769 AN: 3478

ClinVar

ClinVar submissions as Germline

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	-0.79
CADD	Benign	5.5
DANN	Benign	0.56
PhyloP100		-0.22
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: rs2240722; hg19: chr4-10020757; COSMIC: COSV53319049; COSMIC: COSV53319049;