9-27533003-G-T

Position:

• chr9-27533003-G-T

Variant summary

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

The ENST00000645861.1(EMICERI):​n.410+2675G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EMICERI	ENST00000645861.1	n.410+2675G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.0486

Gnomad4 ASJ AF: 0.0404

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.0977

Gnomad4 FIN AF: 0.0459

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.0670

Alfa AF: 0.0648 Hom.: 488

Bravo AF: 0.0598

Asia WGS AF: 0.115 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13290599; hg19: chr9-27533001;