chr20-63743036-C-A

Variant names:

• chr20-63743036-C-A
• rs1058319
• ENST00000493772.5:n.859C>A

Variant summary

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

The ENST00000493772.5(SLC2A4RG):​n.859C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000015 in 1,335,592 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: SLC2A4RG ENST00000493772.5 non_coding_transcript_exon
• 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: 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 (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A4RG	NM_020062.4	c.*46C>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000266077.5	NP_064446.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A4RG	ENST00000493772.5	n.859C>A		non_coding_transcript_exon_variant	Exon 5 of 5	1
SLC2A4RG	ENST00000266077.5	c.*46C>A		3_prime_UTR_variant	Exon 8 of 8	1	NM_020062.4	ENSP00000266077.2
SLC2A4RG	ENST00000473157.1	n.522C>A		non_coding_transcript_exon_variant	Exon 5 of 5	3
SLC2A4RG	ENST00000496425.1	n.421C>A		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome AF: 0.00000150 AC: 2 AN: 1335592 Hom.: 0 Cov.: 21 AF XY: 0.00000305 AC XY: 2 AN XY: 655550

African (AFR) AF: 0.00 AC: 0 AN: 30766

American (AMR) AF: 0.00 AC: 0 AN: 32698

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22492

East Asian (EAS) AF: 0.00 AC: 0 AN: 36774

South Asian (SAS) AF: 0.00 AC: 0 AN: 75376

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45562

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5404

European-Non Finnish (NFE) AF: 9.70e-7 AC: 1 AN: 1031064

Other (OTH) AF: 0.0000180 AC: 1 AN: 55456

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 2321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.9
DANN	Benign	0.60
PhyloP100		0.15

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;