rs563998083
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_022051.3(EGLN1):āc.597G>Cā(p.Val199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,054 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V199V) has been classified as Likely benign.
Frequency
Consequence
NM_022051.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EGLN1 | NM_022051.3 | c.597G>C | p.Val199= | synonymous_variant | 1/5 | ENST00000366641.4 | |
EGLN1 | NM_001377260.1 | c.597G>C | p.Val199= | synonymous_variant | 1/4 | ||
EGLN1 | NM_001377261.1 | c.597G>C | p.Val199= | synonymous_variant | 1/4 | ||
EGLN1 | XM_024447734.2 | c.597G>C | p.Val199= | synonymous_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EGLN1 | ENST00000366641.4 | c.597G>C | p.Val199= | synonymous_variant | 1/5 | 1 | NM_022051.3 | P1 | |
EGLN1 | ENST00000658954.1 | upstream_gene_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247248Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134696
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461054Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726828
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Erythrocytosis, familial, 3 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 25, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | 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 did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 03, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at