11-69328516-A-G

Position:

• chr11-69328516-A-G

Variant summary

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

The ENST00000544781.5(ENSG00000260877):​n.156-12994A>G 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 0.772 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: ENST00000544781.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

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=-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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000544781.5	n.156-12994A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000535660.2	n.305+11591A>G		intron_variant, non_coding_transcript_variant		2
MYEOV	ENST00000544008.1	n.427-12994A>G		intron_variant, non_coding_transcript_variant		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;