11-69328516-A-G

Variant names:

• chr11-69328516-A-G
• rs7102705
• ENST00000535660.2:n.305+11591A>G

Variant summary

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

The ENST00000535660.2(ENSG00000260877):​n.305+11591A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 151,848 control chromosomes in the GnomAD database, including 45,346 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 0.77 (45346 hom., cov: 29)
• Consequence: ENSG00000260877 ENST00000535660.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 16 publications found

Genes affected

ENSG00000260877 (HGNC:):

MYEOV (HGNC:7563): (myeloma overexpressed)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000535660.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260877	ENST00000535660.2	TSL:2	n.305+11591A>G		intron	N/A
	MYEOV	ENST00000544008.1	TSL:2	n.427-12994A>G		intron	N/A
	ENSG00000260877	ENST00000544781.5	TSL:2	n.156-12994A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117111 AN: 151730 Hom.: 45325 Cov.: 29

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.772 AC: 117181 AN: 151848 Hom.: 45346 Cov.: 29 AF XY: 0.773 AC XY: 57361 AN XY: 74234

African (AFR) AF: 0.752 AC: 31090 AN: 41366

American (AMR) AF: 0.710 AC: 10827 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2736 AN: 3468

East Asian (EAS) AF: 0.662 AC: 3373 AN: 5098

South Asian (SAS) AF: 0.825 AC: 3979 AN: 4824

European-Finnish (FIN) AF: 0.837 AC: 8834 AN: 10560

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53841 AN: 67962

Other (OTH) AF: 0.773 AC: 1631 AN: 2110

Alfa AF: 0.782 Hom.: 98888

Bravo AF: 0.758

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.37
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs7102705; hg19: chr11-69143284;