ENST00000645861.1:n.411-2259T>C

Variant names:

• chr9-27533454-T-C
• rs4879541
• ENST00000645861.1:n.411-2259T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000645861.1(EMICERI):​n.411-2259T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,096 control chromosomes in the GnomAD database, including 15,435 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 0.42 (15435 hom., cov: 32)
• Consequence: EMICERI ENST00000645861.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 6 publications found

Genes affected

EMICERI (HGNC:53656): (EQTN MOB3B IFNK C9orf72 enhancer RNA I)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMICERI	ENST00000645861.1	n.411-2259T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64073 AN: 151978 Hom.: 15438 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.421 AC: 64069 AN: 152096 Hom.: 15435 Cov.: 32 AF XY: 0.425 AC XY: 31629 AN XY: 74358

African (AFR) AF: 0.178 AC: 7383 AN: 41522

American (AMR) AF: 0.485 AC: 7414 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2205 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3070 AN: 5168

South Asian (SAS) AF: 0.502 AC: 2419 AN: 4816

European-Finnish (FIN) AF: 0.512 AC: 5408 AN: 10560

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34641 AN: 67956

Other (OTH) AF: 0.440 AC: 930 AN: 2114

Alfa AF: 0.486 Hom.: 20883

Bravo AF: 0.408

Asia WGS AF: 0.474 AC: 1647 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.70
PhyloP100		0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4879541; hg19: chr9-27533452; COSMIC: COSV51788829;