1-231363991-CACAA-C

Variant names:

• chr1-231363991-CACAA-C
• rs574848765
• NM_022051.3:c.*2416_*2419delTTGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_022051.3(EGLN1):​c.*2416_*2419delTTGT variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00173 in 152,198 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0017 (2 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: EGLN1 NM_022051.3 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.79

Genes affected

EGLN1 (HGNC:1232): (egl-9 family hypoxia inducible factor 1) The protein encoded by this gene catalyzes the post-translational formation of 4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins. HIF is a transcriptional complex that plays a central role in mammalian oxygen homeostasis. This protein functions as a cellular oxygen sensor, and under normal oxygen concentration, modification by prolyl hydroxylation is a key regulatory event that targets HIF subunits for proteasomal destruction via the von Hippel-Lindau ubiquitylation complex. Mutations in this gene are associated with erythrocytosis familial type 3 (ECYT3). [provided by RefSeq, Nov 2009]

ENSG00000287856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-231363991-CACAA-C is Benign according to our data. Variant chr1-231363991-CACAA-C is described in ClinVar as [Likely_benign]. Clinvar id is 296144.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00173 (263/152198) while in subpopulation EAS AF= 0.0058 (30/5176). AF 95% confidence interval is 0.00472. There are 2 homozygotes in gnomad4. There are 125 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 263 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EGLN1	NM_022051.3	c.*2416_*2419delTTGT		3_prime_UTR_variant	Exon 5 of 5	ENST00000366641.4	NP_071334.1
EGLN1	NM_001377260.1	c.*2477_*2480delTTGT		3_prime_UTR_variant	Exon 4 of 4		NP_001364189.1
EGLN1	NM_001377261.1	c.*2522_*2525delTTGT		3_prime_UTR_variant	Exon 4 of 4		NP_001364190.1
LOC107985360	XR_001738520.3	n.4098+2608_4098+2611delAACA		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EGLN1	ENST00000366641	c.*2416_*2419delTTGT		3_prime_UTR_variant	Exon 5 of 5	1	NM_022051.3	ENSP00000355601.3
EGLN1	ENST00000667629	c.*2522_*2525delTTGT		3_prime_UTR_variant	Exon 4 of 4			ENSP00000499629.1
ENSG00000287856	ENST00000653908	c.*2522_*2525delTTGT		3_prime_UTR_variant	Exon 5 of 5			ENSP00000499669.1
ENSG00000287856	ENST00000653198.1	n.3239_3242delTTGT		non_coding_transcript_exon_variant	Exon 8 of 8

Frequencies

GnomAD3 genomes AF: 0.00174 AC: 265 AN: 152080 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.00536

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00239

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

GnomAD4 genome AF: 0.00173 AC: 263 AN: 152198 Hom.: 2 Cov.: 33 AF XY: 0.00168 AC XY: 125 AN XY: 74420

Gnomad4 AFR AF: 0.00530

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00580

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000294

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.00178 Hom.: 1

Bravo AF: 0.00160

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial erythrocytosis Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

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: rs574848765; hg19: chr1-231499737;