rs12808959

Variant names:

• chr11-69320083-T-C
• rs12808959
• ENST00000535660.2:n.305+3158T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-69320083-T-C
• chr11-69320083-T-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+3158T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,044 control chromosomes in the GnomAD database, including 16,618 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 0.45 (16618 hom., cov: 33)
• Consequence: ENSG00000260877 ENST00000535660.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260877	ENST00000535660.2	TSL:2	n.305+3158T>C		intron	N/A
	MYEOV	ENST00000544008.1	TSL:2	n.427-21427T>C		intron	N/A
	ENSG00000260877	ENST00000544781.5	TSL:2	n.155+20655T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67680 AN: 151924 Hom.: 16573 Cov.: 33

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.446 AC: 67803 AN: 152044 Hom.: 16618 Cov.: 33 AF XY: 0.450 AC XY: 33460 AN XY: 74314

African (AFR) AF: 0.656 AC: 27208 AN: 41454

American (AMR) AF: 0.447 AC: 6840 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 832 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2268 AN: 5150

South Asian (SAS) AF: 0.382 AC: 1843 AN: 4824

European-Finnish (FIN) AF: 0.470 AC: 4971 AN: 10574

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22655 AN: 67968

Other (OTH) AF: 0.377 AC: 797 AN: 2112

Alfa AF: 0.358 Hom.: 25094

Bravo AF: 0.453

Asia WGS AF: 0.393 AC: 1370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		-0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12808959;

hg19: chr11-69087550;