20-13714909-GCT-G

Position:

• chr20-13714909-GCT-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001276380.2(ESF1):​c.2519_2520del​(p.Glu840AlafsTer21) variant causes a frameshift change. The variant allele was found at a frequency of 0.00266 in 1,610,378 control chromosomes in the GnomAD database, including 11 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0024 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0027 (11 hom.)
• Consequence: ESF1 NM_001276380.2 frameshift
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 6.07

Genes affected

ESF1 (HGNC:15898): (ESF1 nucleolar pre-rRNA processing protein homolog) Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 20-13714909-GCT-G is Benign according to our data. Variant chr20-13714909-GCT-G is described in ClinVar as [Likely_benign]. Clinvar id is 789354.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ESF1	NM_001276380.2	c.2519_2520del	p.Glu840AlafsTer21	frameshift_variant	14/14	ENST00000617257.2	NP_001263309.1
ESF1	NM_016649.4	c.2519_2520del	p.Glu840AlafsTer21	frameshift_variant	14/14		NP_057733.2
ESF1	XM_017027874.3	c.2519_2520del	p.Glu840AlafsTer21	frameshift_variant	14/14		XP_016883363.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ESF1	ENST00000617257.2	c.2519_2520del	p.Glu840AlafsTer21	frameshift_variant	14/14	5	NM_001276380.2	ENSP00000480783	P1
ESF1	ENST00000202816.5	c.2519_2520del	p.Glu840AlafsTer21	frameshift_variant	14/14	5		ENSP00000202816	P1

Frequencies

GnomAD3 genomes AF: 0.00238 AC: 362 AN: 152116 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000628

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00203

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00395

Gnomad OTH AF: 0.00479

GnomAD3 exomes AF: 0.00224 AC: 558 AN: 249610 Hom.: 2 AF XY: 0.00241 AC XY: 325 AN XY: 134896

Gnomad AFR exome AF: 0.000616

Gnomad AMR exome AF: 0.00152

Gnomad ASJ exome AF: 0.00339

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000332

Gnomad FIN exome AF: 0.00176

Gnomad NFE exome AF: 0.00346

Gnomad OTH exome AF: 0.00363

GnomAD4 exome AF: 0.00269 AC: 3918 AN: 1458144 Hom.: 11 AF XY: 0.00257 AC XY: 1862 AN XY: 725150

Gnomad4 AFR exome AF: 0.000301

Gnomad4 AMR exome AF: 0.00172

Gnomad4 ASJ exome AF: 0.00288

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000340

Gnomad4 FIN exome AF: 0.00263

Gnomad4 NFE exome AF: 0.00307

Gnomad4 OTH exome AF: 0.00249

GnomAD4 genome AF: 0.00237 AC: 361 AN: 152234 Hom.: 0 Cov.: 32 AF XY: 0.00208 AC XY: 155 AN XY: 74442

Gnomad4 AFR AF: 0.000626

Gnomad4 AMR AF: 0.00203

Gnomad4 ASJ AF: 0.00433

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00394

Gnomad4 OTH AF: 0.00474

Alfa AF: 0.00265 Hom.: 0

Bravo AF: 0.00221

EpiCase AF: 0.00378

EpiControl AF: 0.00392

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

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: rs534749610; hg19: chr20-13695556;