chr20-63740028-C-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020062.4(SLC2A4RG):​c.116C>A​(p.Thr39Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC2A4RG NM_020062.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.051805228).

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>A	p.Thr39Lys	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>A	p.Thr39Lys	missense	Exon 1 of 8	ENSP00000266077.2	Q9NR83-1
	ENSG00000273047	ENST00000467211.1	TSL:3	c.229-349C>A		intron	N/A	ENSP00000477118.1	V9GYV3
	SLC2A4RG	ENST00000946584.1		c.116C>A	p.Thr39Lys	missense	Exon 1 of 8	ENSP00000616643.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 834634 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 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: 0.00 AC: 0 AN: 762282

Other (OTH) AF: 0.00 AC: 0 AN: 27396

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	18
DANN	Benign	0.84
DEOGEN2	Benign	0.075	T
Eigen	Benign	-0.96
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.015	N
LIST_S2	Benign	0.28	T
M_CAP	Benign	0.033	D
MetaRNN	Benign	0.052	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		-1.2
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-0.66	N
REVEL	Benign	0.053
Sift	Uncertain	0.025	D
Sift4G	Benign	0.14	T
Polyphen		0.52	P
Vest4		0.095
MutPred		0.20		Loss of phosphorylation at T39 (P = 0.007)
MVP		0.076
MPC		0.069
ClinPred		0.12	T
GERP RS		0.61
PromoterAI		-0.022	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.3
Varity_R		0.070
gMVP		0.17
Mutation Taster		=98/2	polymorphism

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: rs1200532060; hg19: chr20-62371381;