rs10812610

Positions:

• chr9-27533986-C-A
• chr9-27533986-C-T

Variant summary

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

The ENST00000645861.1(EMICERI):​n.411-1727C>A 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 0.442 in 151,808 control chromosomes in the GnomAD database, including 16,056 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 0.44 (16056 hom., cov: 31)
• Consequence: EMICERI ENST00000645861.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 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.411-1727C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67030 AN: 151690 Hom.: 16058 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.442 AC: 67037 AN: 151808 Hom.: 16056 Cov.: 31 AF XY: 0.446 AC XY: 33068 AN XY: 74190

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.451

Alfa AF: 0.506 Hom.: 28751

Bravo AF: 0.431

Asia WGS AF: 0.479 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.35
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10812610; hg19: chr9-27533984; COSMIC: COSV51788834;