1-44234176-T-G

Variant names:

• chr1-44234176-T-G
• rs17414912
• NM_024066.3:c.932-12536A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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:41431): (ERI3 intronic transcript 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024066.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERI3	NM_024066.3	MANE Select	c.932-12536A>C		intron	N/A	NP_076971.1	O43414-1
	ERI3	NM_001301698.2		c.698-12536A>C		intron	N/A	NP_001288627.1
	ERI3	NM_001301699.1		c.698-12536A>C		intron	N/A	NP_001288628.1	O43414

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERI3	ENST00000372257.7	TSL:1 MANE Select	c.932-12536A>C		intron	N/A	ENSP00000361331.2	O43414-1
	ERI3	ENST00000930637.1		c.1043-12536A>C		intron	N/A	ENSP00000600696.1
	ERI3	ENST00000930636.1		c.1040-12536A>C		intron	N/A	ENSP00000600695.1

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

African (AFR) AF: 0.0953 AC: 3960 AN: 41536

American (AMR) AF: 0.261 AC: 3989 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3472

East Asian (EAS) AF: 0.236 AC: 1220 AN: 5160

South Asian (SAS) AF: 0.402 AC: 1942 AN: 4828

European-Finnish (FIN) AF: 0.236 AC: 2495 AN: 10566

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13996 AN: 68006

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.202 Hom.: 5564

Bravo AF: 0.182

Asia WGS AF: 0.351 AC: 1220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.8
DANN	Benign	0.77
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17414912; hg19: chr1-44699848;