rs80359850

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001017420.3(ESCO2):​c.604C>G​(p.Gln202Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

ESCO2
NM_001017420.3 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.753
Variant links:
Genes affected
ESCO2 (HGNC:27230): (establishment of sister chromatid cohesion N-acetyltransferase 2) This gene encodes a protein that may have acetyltransferase activity and may be required for the establishment of sister chromatid cohesion during the S phase of mitosis. Mutations in this gene have been associated with Roberts syndrome. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19148433).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ESCO2NM_001017420.3 linkc.604C>G p.Gln202Glu missense_variant Exon 3 of 11 ENST00000305188.13 NP_001017420.1 Q56NI9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ESCO2ENST00000305188.13 linkc.604C>G p.Gln202Glu missense_variant Exon 3 of 11 1 NM_001017420.3 ENSP00000306999.8 Q56NI9-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.39
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.13
T
Eigen
Uncertain
0.33
Eigen_PC
Uncertain
0.40
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Benign
0.75
T
M_CAP
Benign
0.025
D
MetaRNN
Benign
0.19
T
MetaSVM
Benign
-0.60
T
MutationAssessor
Uncertain
2.0
M
PrimateAI
Benign
0.31
T
PROVEAN
Benign
-0.71
N
REVEL
Benign
0.092
Sift
Benign
0.073
T
Sift4G
Benign
0.10
T
Polyphen
0.39
B
Vest4
0.20
MutPred
0.22
Gain of ubiquitination at K200 (P = 0.0303);
MVP
0.78
MPC
0.19
ClinPred
0.53
D
GERP RS
4.9
Varity_R
0.14
gMVP
0.50

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-27634429; API