20-63743036-C-T

Position:

• chr20-63743036-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A4RG	NM_020062.4	c.*46C>T		3_prime_UTR_variant	8/8	ENST00000266077.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A4RG	ENST00000266077.5	c.*46C>T		3_prime_UTR_variant	8/8	1	NM_020062.4	P1
SLC2A4RG	ENST00000493772.5	n.859C>T		non_coding_transcript_exon_variant	5/5	1
SLC2A4RG	ENST00000473157.1	n.522C>T		non_coding_transcript_exon_variant	5/5	3
SLC2A4RG	ENST00000496425.1	n.421C>T		non_coding_transcript_exon_variant	2/2	2

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

GnomAD3 exomes AF: 0.209 AC: 30860 AN: 147906 Hom.: 4669 AF XY: 0.210 AC XY: 16629 AN XY: 79058

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 SAS exome AF: 0.266

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

Gnomad4 AFR exome AF: 0.0383

Gnomad4 AMR exome AF: 0.218

Gnomad4 ASJ exome AF: 0.208

Gnomad4 EAS exome AF: 0.592

Gnomad4 SAS exome AF: 0.255

Gnomad4 FIN exome AF: 0.124

Gnomad4 NFE exome AF: 0.139

Gnomad4 OTH exome AF: 0.178

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

Gnomad4 AFR AF: 0.0450

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.159

Alfa AF: 0.134 Hom.: 1604

Bravo AF: 0.138

Asia WGS AF: 0.398 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.55

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: rs1058319; hg19: chr20-62374389;