1-231364350-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_022051.3(EGLN1):c.*2061C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 152,314 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_022051.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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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.*2061C>G | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000366641.4 | NP_071334.1 | ||
EGLN1 | NM_001377260.1 | c.*2122C>G | 3_prime_UTR_variant | Exon 4 of 4 | NP_001364189.1 | |||
EGLN1 | NM_001377261.1 | c.*2167C>G | 3_prime_UTR_variant | Exon 4 of 4 | NP_001364190.1 | |||
LOC107985360 | XR_001738520.3 | n.4098+2963G>C | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGLN1 | ENST00000366641 | c.*2061C>G | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_022051.3 | ENSP00000355601.3 | |||
EGLN1 | ENST00000667629 | c.*2167C>G | 3_prime_UTR_variant | Exon 4 of 4 | ENSP00000499629.1 | |||||
ENSG00000287856 | ENST00000653908 | c.*2167C>G | 3_prime_UTR_variant | Exon 5 of 5 | ENSP00000499669.1 | |||||
ENSG00000287856 | ENST00000653198.1 | n.2884C>G | non_coding_transcript_exon_variant | Exon 8 of 8 |
Frequencies
GnomAD3 genomes AF: 0.0149 AC: 2272AN: 152196Hom.: 56 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 4Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 4
GnomAD4 genome AF: 0.0149 AC: 2273AN: 152314Hom.: 56 Cov.: 33 AF XY: 0.0143 AC XY: 1067AN XY: 74470
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 was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at