20-13715482-G-C

Variant names:

• chr20-13715482-G-C
• rs6042314
• NM_001276380.2:c.2263-315C>G

Variant summary

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

The NM_001276380.2(ESF1):​c.2263-315C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,018 control chromosomes in the GnomAD database, including 41,920 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 0.74 (41920 hom., cov: 30)
• Consequence: ESF1 NM_001276380.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ESF1	NM_001276380.2	c.2263-315C>G		intron_variant	Intron 13 of 13	ENST00000617257.2	NP_001263309.1
ESF1	NM_016649.4	c.2263-315C>G		intron_variant	Intron 13 of 13		NP_057733.2
ESF1	XM_017027874.3	c.2263-315C>G		intron_variant	Intron 13 of 13		XP_016883363.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ESF1	ENST00000617257.2	c.2263-315C>G		intron_variant	Intron 13 of 13	5	NM_001276380.2	ENSP00000480783.2
ESF1	ENST00000202816.5	c.2263-315C>G		intron_variant	Intron 13 of 13	5		ENSP00000202816.1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112193 AN: 151900 Hom.: 41911 Cov.: 30

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.738 AC: 112237 AN: 152018 Hom.: 41920 Cov.: 30 AF XY: 0.744 AC XY: 55280 AN XY: 74282

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.786

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.758

Alfa AF: 0.670 Hom.: 1999

Bravo AF: 0.730

Asia WGS AF: 0.911 AC: 3168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.57
DANN	Benign	0.41

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: rs6042314; hg19: chr20-13696129;