1-44234176-T-G

Position:

• chr1-44234176-T-G

Variant summary

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

The NM_024066.3(ERI3):​c.932-12536A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,160 control chromosomes in the GnomAD database, including 3,140 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 0.19 (3140 hom., cov: 31)
• Consequence: ERI3 NM_024066.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERI3	NM_024066.3	c.932-12536A>C		intron_variant		ENST00000372257.7	NP_076971.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERI3	ENST00000372257.7	c.932-12536A>C		intron_variant		1	NM_024066.3	ENSP00000361331.2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28626 AN: 152042 Hom.: 3126 Cov.: 31

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.188 AC: 28654 AN: 152160 Hom.: 3140 Cov.: 31 AF XY: 0.195 AC XY: 14481 AN XY: 74358

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.172

Alfa AF: 0.205 Hom.: 4504

Bravo AF: 0.182

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.8
DANN	Benign	0.77

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: rs17414912; hg19: chr1-44699848;