chr18-21540013-G-GAT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_052911.3(ESCO1):c.1954-5_1954-4insAT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0064 ( 8 hom., cov: 0)
Exomes 𝑓: 0.0036 ( 0 hom. )
Consequence
ESCO1
NM_052911.3 splice_region, splice_polypyrimidine_tract, intron
NM_052911.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.640
Genes affected
ESCO1 (HGNC:24645): (establishment of sister chromatid cohesion N-acetyltransferase 1) Enables identical protein binding activity; peptide-lysine-N-acetyltransferase activity; and zinc ion binding activity. Involved in peptidyl-lysine acetylation; post-translational protein acetylation; and regulation of DNA replication. Located in chromatin. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 18-21540013-G-GAT is Benign according to our data. Variant chr18-21540013-G-GAT is described in ClinVar as [Benign]. Clinvar id is 716495.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00642 (952/148274) while in subpopulation AFR AF= 0.0188 (758/40378). AF 95% confidence interval is 0.0177. There are 8 homozygotes in gnomad4. There are 457 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High AC in GnomAd at 947 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ESCO1 | NM_052911.3 | c.1954-5_1954-4insAT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000269214.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESCO1 | ENST00000269214.10 | c.1954-5_1954-4insAT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_052911.3 | P1 | |||
ESCO1 | ENST00000622333.1 | c.-51-5_-51-4insAT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
ESCO1 | ENST00000383276.1 | c.2078-5_2078-4insAT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00639 AC: 947AN: 148182Hom.: 8 Cov.: 0
GnomAD3 genomes
?
AF:
AC:
947
AN:
148182
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00319 AC: 426AN: 133396Hom.: 0 AF XY: 0.00311 AC XY: 227AN XY: 73092
GnomAD3 exomes
AF:
AC:
426
AN:
133396
Hom.:
AF XY:
AC XY:
227
AN XY:
73092
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00360 AC: 3976AN: 1104026Hom.: 0 Cov.: 0 AF XY: 0.00351 AC XY: 1952AN XY: 556168
GnomAD4 exome
AF:
AC:
3976
AN:
1104026
Hom.:
Cov.:
0
AF XY:
AC XY:
1952
AN XY:
556168
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00642 AC: 952AN: 148274Hom.: 8 Cov.: 0 AF XY: 0.00633 AC XY: 457AN XY: 72154
GnomAD4 genome
?
AF:
AC:
952
AN:
148274
Hom.:
Cov.:
0
AF XY:
AC XY:
457
AN XY:
72154
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 19, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at