rs1958589

Positions:

• chr14-34375170-T-C

Variant summary

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

The variant allele was found at a frequency of 0.208 in 152,154 control chromosomes in the GnomAD database, including 4,062 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 0.21 (4062 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.34375170T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EGLN3	ENST00000551935.5	n.59+87546A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31548 AN: 152036 Hom.: 4053 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.0962

Gnomad SAS AF: 0.0956

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.208 AC: 31594 AN: 152154 Hom.: 4062 Cov.: 32 AF XY: 0.211 AC XY: 15676 AN XY: 74400

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.0952

Gnomad4 SAS AF: 0.0965

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.161

Alfa AF: 0.154 Hom.: 1485

Bravo AF: 0.219

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	6.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1958589; hg19: chr14-34844376;