9-27533003-G-T

Variant names:

• chr9-27533003-G-T
• rs13290599
• ENST00000645861.1:n.410+2675G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000645861.1(EMICERI):​n.410+2675G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0617 in 152,126 control chromosomes in the GnomAD database, including 327 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 0.062 (327 hom., cov: 32)
• Consequence: EMICERI ENST00000645861.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645861.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EMICERI	ENST00000645861.1		n.410+2675G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0617 AC: 9376 AN: 152008 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0485

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.0459

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.0634

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

GnomAD4 genome AF: 0.0617 AC: 9386 AN: 152126 Hom.: 327 Cov.: 32 AF XY: 0.0604 AC XY: 4491 AN XY: 74372

African (AFR) AF: 0.0520 AC: 2157 AN: 41494

American (AMR) AF: 0.0486 AC: 744 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3468

East Asian (EAS) AF: 0.110 AC: 568 AN: 5170

South Asian (SAS) AF: 0.0977 AC: 471 AN: 4820

European-Finnish (FIN) AF: 0.0459 AC: 486 AN: 10590

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4625 AN: 67978

Other (OTH) AF: 0.0670 AC: 141 AN: 2104

Alfa AF: 0.0639 Hom.: 609

Bravo AF: 0.0598

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.45
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs13290599; hg19: chr9-27533001;