20-63743036-C-T

Variant names:

• chr20-63743036-C-T
• rs1058319
• NM_020062.4:c.*46C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 36 publications found

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]

ACMG classification

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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.: 30

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

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.: 21 AF XY: 0.163 AC XY: 106731 AN XY: 655142

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

GnomAD4 genome AF: 0.136 AC: 20634 AN: 151854 Hom.: 2283 Cov.: 30 AF XY: 0.141 AC XY: 10476 AN XY: 74218

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: 49 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9122 AN: 67820

Other (OTH) AF: 0.159 AC: 336 AN: 2108

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
DANN	Benign	0.55
PhyloP100		0.15
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: rs1058319; hg19: chr20-62374389;