chr18-21564221-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_052911.3(ESCO1):c.1803T>G(p.Asp601Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000896 in 1,450,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
Genome browser will be placed here
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.1803T>G | p.Asp601Glu | missense_variant | 7/12 | ENST00000269214.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESCO1 | ENST00000269214.10 | c.1803T>G | p.Asp601Glu | missense_variant | 7/12 | 1 | NM_052911.3 | P1 | |
ESCO1 | ENST00000383276.1 | c.1803T>G | p.Asp601Glu | missense_variant, NMD_transcript_variant | 7/13 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000168 AC: 4AN: 238726Hom.: 0 AF XY: 0.0000155 AC XY: 2AN XY: 128882
GnomAD4 exome AF: 0.00000896 AC: 13AN: 1450120Hom.: 0 Cov.: 29 AF XY: 0.00000971 AC XY: 7AN XY: 720922
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 28, 2022 | The c.1803T>G (p.D601E) alteration is located in exon 7 (coding exon 4) of the ESCO1 gene. This alteration results from a T to G substitution at nucleotide position 1803, causing the aspartic acid (D) at amino acid position 601 to be replaced by a glutamic acid (E). 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