rs12808959

Positions:

• chr11-69320083-T-C
• chr11-69320083-T-G

Variant summary

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

The ENST00000544781.5(ENSG00000260877):​n.155+20655T>C 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 0.446 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: ENST00000544781.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

Genes affected

(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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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
	ENST00000544781.5	n.155+20655T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000535660.2	n.305+3158T>C		intron_variant, non_coding_transcript_variant		2
MYEOV	ENST00000544008.1	n.427-21427T>C		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.377

Alfa AF: 0.341 Hom.: 15706

Bravo AF: 0.453

Asia WGS AF: 0.393 AC: 1370 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12808959; hg19: chr11-69087550;