rs4660781

chr1-44235092-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_024066.3(ERI3):c.931+12847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0334 in 152,302 control chromosomes in the GnomAD database, including 111 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 0.033 (111 hom., cov: 31)
• Consequence: ERI3 NM_024066.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

Genes affected

ERI3 (HGNC:17276): (ERI1 exoribonuclease family member 3) Enables RNA binding activity. Predicted to be involved in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). [provided by Alliance of Genome Resources, Apr 2022]

ERI3-IT1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0334 (5093/152302) while in subpopulation SAS AF= 0.0435 (210/4826). AF 95% confidence interval is 0.0395. There are 111 homozygotes in gnomad4. There are 2528 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 111 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERI3	NM_024066.3	c.931+12847T>C		intron_variant		ENST00000372257.7
ERI3-IT1	NR_110056.1	n.205+6823T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERI3	ENST00000372257.7	c.931+12847T>C		intron_variant		1	NM_024066.3	P1

Frequencies

GnomAD3 genomes AF: 0.0335 AC: 5095 AN: 152184 Hom.: 111 Cov.: 31

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0257

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0355

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

GnomAD4 genome AF: 0.0334 AC: 5093 AN: 152302 Hom.: 111 Cov.: 31 AF XY: 0.0339 AC XY: 2528 AN XY: 74480

Gnomad4 AFR AF: 0.0170

Gnomad4 AMR AF: 0.0257

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0435

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0408

Gnomad4 OTH AF: 0.0351

Alfa AF: 0.0405 Hom.: 79

Bravo AF: 0.0305

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.1
Dann	Benign	0.83

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: rs4660781; hg19: chr1-44700764;