chr1-231366433-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000366641.4(EGLN1):c.1259C>T(p.Ser420Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000262 in 1,613,556 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. S420S) has been classified as Likely benign.
Frequency
Consequence
ENST00000366641.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EGLN1 | NM_022051.3 | c.1259C>T | p.Ser420Leu | missense_variant | 5/5 | ENST00000366641.4 | NP_071334.1 | |
LOC107985360 | XR_001738520.3 | n.4099-3121G>A | intron_variant, non_coding_transcript_variant | |||||
EGLN1 | NM_001377260.1 | c.*39C>T | 3_prime_UTR_variant | 4/4 | NP_001364189.1 | |||
EGLN1 | NM_001377261.1 | c.*84C>T | 3_prime_UTR_variant | 4/4 | NP_001364190.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EGLN1 | ENST00000366641.4 | c.1259C>T | p.Ser420Leu | missense_variant | 5/5 | 1 | NM_022051.3 | ENSP00000355601 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000448 AC: 68AN: 151748Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000660 AC: 166AN: 251424Hom.: 1 AF XY: 0.000648 AC XY: 88AN XY: 135882
GnomAD4 exome AF: 0.000242 AC: 354AN: 1461808Hom.: 1 Cov.: 30 AF XY: 0.000227 AC XY: 165AN XY: 727208
GnomAD4 genome AF: 0.000448 AC: 68AN: 151748Hom.: 0 Cov.: 32 AF XY: 0.000648 AC XY: 48AN XY: 74064
ClinVar
Submissions by phenotype
Erythrocytosis, familial, 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at