NM_022051.3:c.*2043C>T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_022051.3(EGLN1):c.*2043C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00139 in 152,302 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_022051.3 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EGLN1 | NM_022051.3 | c.*2043C>T | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000366641.4 | NP_071334.1 | ||
EGLN1 | NM_001377260.1 | c.*2104C>T | 3_prime_UTR_variant | Exon 4 of 4 | NP_001364189.1 | |||
EGLN1 | NM_001377261.1 | c.*2149C>T | 3_prime_UTR_variant | Exon 4 of 4 | NP_001364190.1 | |||
LOC107985360 | XR_001738520.3 | n.4098+2981G>A | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGLN1 | ENST00000366641 | c.*2043C>T | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_022051.3 | ENSP00000355601.3 | |||
EGLN1 | ENST00000667629 | c.*2149C>T | 3_prime_UTR_variant | Exon 4 of 4 | ENSP00000499629.1 | |||||
ENSG00000287856 | ENST00000653908 | c.*2149C>T | 3_prime_UTR_variant | Exon 5 of 5 | ENSP00000499669.1 | |||||
ENSG00000287856 | ENST00000653198.1 | n.2866C>T | non_coding_transcript_exon_variant | Exon 8 of 8 |
Frequencies
GnomAD3 genomes AF: 0.00140 AC: 213AN: 152184Hom.: 1 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 16Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 14
GnomAD4 genome AF: 0.00139 AC: 212AN: 152302Hom.: 1 Cov.: 33 AF XY: 0.00120 AC XY: 89AN XY: 74464
ClinVar
Submissions by phenotype
Erythrocytosis, familial, 3 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at