11-69328516-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000260877 (HGNC:):

MYEOV (HGNC:7563): (myeloma overexpressed)

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000260877	ENST00000535660.2	n.305+11591A>G		intron_variant	Intron 3 of 3	2
MYEOV	ENST00000544008.1	n.427-12994A>G		intron_variant	Intron 1 of 1	2
ENSG00000260877	ENST00000544781.5	n.156-12994A>G		intron_variant	Intron 1 of 2	2

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

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.773

Alfa AF: 0.786 Hom.: 59526

Bravo AF: 0.758

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7102705; hg19: chr11-69143284;