11-69328516-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.220
Variant links:
Genes affected
MYEOV (HGNC:7563): (myeloma overexpressed)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
ENSG00000260877ENST00000535660.2 linkn.305+11591A>G intron_variant Intron 3 of 3 2
MYEOVENST00000544008.1 linkn.427-12994A>G intron_variant Intron 1 of 1 2
ENSG00000260877ENST00000544781.5 linkn.156-12994A>G intron_variant Intron 1 of 2 2

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7102705; hg19: chr11-69143284; API