chr20-63740028-C-T

Variant names:

• chr20-63740028-C-T
• rs1200532060
• NM_020062.4:c.116C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020062.4(SLC2A4RG):​c.116C>T​(p.Thr39Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000408 in 980,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T39K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000068 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000036 (0 hom.)
• Consequence: SLC2A4RG NM_020062.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 0 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]

ENSG00000273047 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08025095).

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.116C>T	p.Thr39Met	missense	Exon 1 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.116C>T	p.Thr39Met	missense	Exon 1 of 8	ENSP00000266077.2	Q9NR83-1
	ENSG00000273047	ENST00000467211.1	TSL:3	c.229-349C>T		intron	N/A	ENSP00000477118.1	V9GYV3
	SLC2A4RG	ENST00000946584.1		c.116C>T	p.Thr39Met	missense	Exon 1 of 8	ENSP00000616643.1

Frequencies

GnomAD3 genomes AF: 0.00000684 AC: 1 AN: 146292 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000152

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000359 AC: 3 AN: 834634 Hom.: 0 Cov.: 27 AF XY: 0.00000259 AC XY: 1 AN XY: 385612

African (AFR) AF: 0.00 AC: 0 AN: 15806

American (AMR) AF: 0.00 AC: 0 AN: 1058

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5190

East Asian (EAS) AF: 0.00 AC: 0 AN: 3676

South Asian (SAS) AF: 0.00 AC: 0 AN: 17074

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 390

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1762

European-Non Finnish (NFE) AF: 0.00000262 AC: 2 AN: 762282

Other (OTH) AF: 0.0000365 AC: 1 AN: 27396

GnomAD4 genome AF: 0.00000684 AC: 1 AN: 146292 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 71144

African (AFR) AF: 0.00 AC: 0 AN: 40812

American (AMR) AF: 0.00 AC: 0 AN: 14754

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3392

East Asian (EAS) AF: 0.00 AC: 0 AN: 5064

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8418

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.0000152 AC: 1 AN: 65804

Other (OTH) AF: 0.00 AC: 0 AN: 2012

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.61
CADD	Benign	18
DANN	Benign	0.97
DEOGEN2	Benign	0.072	T
Eigen	Benign	-0.78
Eigen_PC	Benign	-0.93
FATHMM_MKL	Benign	0.0094	N
LIST_S2	Benign	0.42	T
M_CAP	Benign	0.039	D
MetaRNN	Benign	0.080	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		-1.2
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-0.59	N
REVEL	Benign	0.074
Sift	Uncertain	0.011	D
Sift4G	Uncertain	0.037	D
Polyphen		0.98	D
Vest4		0.14
MutPred		0.21		Loss of glycosylation at T39 (P = 0.0025)
MVP		0.13
MPC		0.061
ClinPred		0.18	T
GERP RS		0.61
PromoterAI		-0.031	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.3
Varity_R		0.038
gMVP		0.18
Mutation Taster		=98/2	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1200532060; hg19: chr20-62371381;