Genetic Variant SLC2A4RG:c.*46C>T (chr20-63743036-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020062.4(SLC2A4RG):c.*46C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,486,632 control chromosomes in the GnomAD database, including 24,389 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 2283 hom., cov: 30)

Exomes 𝑓: 0.16 ( 22106 hom. )

Consequence

SLC2A4RG
NM_020062.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.152

Publications

36 publications found

Variant links:

Genes affected

SLC2A4RG (HGNC:15930): (SLC2A4 regulator) The protein encoded by this gene is a nuclear transcription factor involved in the activation of the solute carrier family 2 member 4 gene. The encoded protein interacts with another transcription factor, myocyte enhancer factor 2, to activate transcription of this gene. [provided by RefSeq, Jul 2008]

SLC2A4RG links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_020062.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020062.4. 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
	SLC2A4RG	NM_020062.4	MANE Select	c.*46C>T		3_prime_UTR	Exon 8 of 8	NP_064446.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC2A4RG	ENST00000266077.5	TSL:1 MANE Select	c.*46C>T	3_prime_UTR	Exon 8 of 8	ENSP00000266077.2	Q9NR83-1
SLC2A4RG	ENST00000493772.5	TSL:1	n.859C>T	non_coding_transcript_exon	Exon 5 of 5
SLC2A4RG	ENST00000946584.1		c.*46C>T	3_prime_UTR	Exon 8 of 8	ENSP00000616643.1

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20629

AN:

151736

Hom.:

2281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0451

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.206

Gnomad EAS

AF:

0.602

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.121

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.155

GnomAD2 exomes

AF:

0.209

AC:

30860

AN:

147906

AF XY:

0.210

show subpopulations

Gnomad AFR exome

AF:

0.0405

Gnomad AMR exome

AF:

0.224

Gnomad ASJ exome

AF:

0.216

Gnomad EAS exome

AF:

0.625

Gnomad FIN exome

AF:

0.129

Gnomad NFE exome

AF:

0.142

Gnomad OTH exome

AF:

0.193

GnomAD4 exome

AF:

0.160

AC:

213345

AN:

1334778

Hom.:

22106

Cov.:

AF XY:

0.163

AC XY:

106731

AN XY:

655142

show subpopulations

African (AFR)

AF:

0.0383

AC:

1179

AN:

30762

American (AMR)

AF:

0.218

AC:

7105

AN:

32662

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

4677

AN:

22460

East Asian (EAS)

AF:

0.592

AC:

21765

AN:

36744

South Asian (SAS)

AF:

0.255

AC:

19173

AN:

75318

European-Finnish (FIN)

AF:

0.124

AC:

5650

AN:

45534

Middle Eastern (MID)

AF:

0.194

AC:

1050

AN:

5400

European-Non Finnish (NFE)

AF:

0.139

AC:

142863

AN:

1030466

Other (OTH)

AF:

0.178

AC:

9883

AN:

55432

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

8272

16544

24815

33087

41359

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5566

11132

16698

22264

27830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.136

AC:

20634

AN:

151854

Hom.:

2283

Cov.:

AF XY:

0.141

AC XY:

10476

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.0450

AC:

1867

AN:

41492

American (AMR)

AF:

0.183

AC:

2794

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.206

AC:

716

AN:

3468

East Asian (EAS)

AF:

0.602

AC:

3066

AN:

5094

South Asian (SAS)

AF:

0.271

AC:

1304

AN:

4810

European-Finnish (FIN)

AF:

0.121

AC:

1278

AN:

10576

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.135

AC:

9122

AN:

67820

Other (OTH)

AF:

0.159

AC:

336

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

812

1623

2435

3246

4058

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

230

460

690

920

1150

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.134

Hom.:

2321

Bravo

AF:

0.138

Asia WGS

AF:

0.398

AC:

1383

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.7

(source)

DANN

Benign

0.55

PhyloP100

0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over