rs10812610

Variant names:

• chr9-27533986-C-A
• rs10812610
• ENST00000645861.1:n.411-1727C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000645861.1(EMICERI):​n.411-1727C>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 30 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=-0.85).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EMICERI	ENST00000645861.1	n.411-1727C>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.249 AC: 10283 AN: 41370

American (AMR) AF: 0.493 AC: 7521 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2203 AN: 3468

East Asian (EAS) AF: 0.592 AC: 3059 AN: 5164

South Asian (SAS) AF: 0.507 AC: 2441 AN: 4810

European-Finnish (FIN) AF: 0.514 AC: 5396 AN: 10500

Middle Eastern (MID) AF: 0.503 AC: 146 AN: 290

European-Non Finnish (NFE) AF: 0.509 AC: 34585 AN: 67940

Other (OTH) AF: 0.451 AC: 950 AN: 2108

Alfa AF: 0.488 Hom.: 40603

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

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