rs712300

Variant names:

• chr14-34061733-G-A
• rs712300
• ENST00000487915.6:c.3+30588C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-34061733-G-A
• chr14-34061733-G-C
• chr14-34061733-G-T

Variant summary

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

The NR_184209.1(EGLN3-AS1):​n.2857G>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 0.756 in 151,832 control chromosomes in the GnomAD database, including 43,793 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 0.76 (43793 hom., cov: 30)
• Consequence: EGLN3-AS1 NR_184209.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 2 publications found

Genes affected

EGLN3 (HGNC:14661): (egl-9 family hypoxia inducible factor 3) Enables peptidyl-proline 4-dioxygenase activity. Involved in several processes, including activation of cysteine-type endopeptidase activity involved in apoptotic process; peptidyl-proline hydroxylation to 4-hydroxy-L-proline; and response to hypoxia. Located in cytosol and nucleus. Implicated in renal cell carcinoma. Biomarker of clear cell renal cell carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

EGLN3-AS1 (HGNC:49077): (EGLN3 antisense RNA 1)

ENSG00000308531 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_184209.1. 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
	EGLN3-AS1	NR_184209.1		n.2857G>A		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EGLN3	ENST00000487915.6	TSL:5	c.3+30588C>T		intron	N/A	ENSP00000451316.1	G3V3M1
	EGLN3	ENST00000551935.5	TSL:4	n.297+30588C>T		intron	N/A
	ENSG00000308531	ENST00000834813.1		n.91+231G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114646 AN: 151714 Hom.: 43745 Cov.: 30

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.771

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.756 AC: 114755 AN: 151832 Hom.: 43793 Cov.: 30 AF XY: 0.760 AC XY: 56343 AN XY: 74168

African (AFR) AF: 0.805 AC: 33298 AN: 41388

American (AMR) AF: 0.799 AC: 12201 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2778 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5131 AN: 5152

South Asian (SAS) AF: 0.752 AC: 3622 AN: 4814

European-Finnish (FIN) AF: 0.693 AC: 7259 AN: 10482

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47997 AN: 67956

Other (OTH) AF: 0.773 AC: 1628 AN: 2106

Alfa AF: 0.732 Hom.: 15101

Bravo AF: 0.766

Asia WGS AF: 0.885 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.43
PhyloP100		-0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs712300; hg19: chr14-34530939;