18-21554414-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052911.3(ESCO1):c.1953+6445T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,072 control chromosomes in the GnomAD database, including 21,557 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (21557 hom., cov: 32)
• Consequence: ESCO1 NM_052911.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ESCO1	NM_052911.3	c.1953+6445T>A		intron_variant		ENST00000269214.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ESCO1	ENST00000269214.10	c.1953+6445T>A		intron_variant		1	NM_052911.3	P1
ESCO1	ENST00000622333.1	c.-176+6445T>A		intron_variant		2
ESCO1	ENST00000383276.1	c.1953+6445T>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75682 AN: 151952 Hom.: 21512 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.482

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.498 AC: 75788 AN: 152072 Hom.: 21557 Cov.: 32 AF XY: 0.501 AC XY: 37241 AN XY: 74330

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.484

Alfa AF: 0.231 Hom.: 454

Bravo AF: 0.521

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.94
Dann	Benign	0.27

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

LitVar

Other links and lift over

dbSNP: rs4800795; hg19: chr18-19134375;