rs1680695

Positions:

• chr14-33938877-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022073.4(EGLN3):​c.358-7662A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,074 control chromosomes in the GnomAD database, including 6,303 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 0.27 (6303 hom., cov: 32)
• Consequence: EGLN3 NM_022073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EGLN3	NM_022073.4	c.358-7662A>C		intron_variant		ENST00000250457.9	NP_071356.1
EGLN3	NM_001308103.2	c.76-7662A>C		intron_variant			NP_001295032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EGLN3	ENST00000250457.9	c.358-7662A>C		intron_variant		1	NM_022073.4	ENSP00000250457.4
EGLN3	ENST00000553215.5	c.76-7662A>C		intron_variant		1		ENSP00000447470.1
EGLN3	ENST00000487915.6	c.4-7662A>C		intron_variant		5		ENSP00000451316.1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40677 AN: 151956 Hom.: 6301 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.268 AC: 40684 AN: 152074 Hom.: 6303 Cov.: 32 AF XY: 0.262 AC XY: 19474 AN XY: 74326

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.260

Alfa AF: 0.310 Hom.: 1782

Bravo AF: 0.253

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.81

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: rs1680695; hg19: chr14-34408083;