18-21573831-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_052911.3(ESCO1):c.1013A>G(p.Glu338Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000905 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_052911.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ESCO1 | NM_052911.3 | c.1013A>G | p.Glu338Gly | missense_variant | 4/12 | ENST00000269214.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESCO1 | ENST00000269214.10 | c.1013A>G | p.Glu338Gly | missense_variant | 4/12 | 1 | NM_052911.3 | P1 | |
ESCO1 | ENST00000383276.1 | c.1013A>G | p.Glu338Gly | missense_variant, NMD_transcript_variant | 4/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250654Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135674
GnomAD4 exome AF: 0.0000992 AC: 145AN: 1461670Hom.: 0 Cov.: 59 AF XY: 0.000102 AC XY: 74AN XY: 727160
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2023 | The c.1013A>G (p.E338G) alteration is located in exon 4 (coding exon 1) of the ESCO1 gene. This alteration results from a A to G substitution at nucleotide position 1013, causing the glutamic acid (E) at amino acid position 338 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at