16-89971748-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NR_172519.1(CENPBD1P):​n.749G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,460,408 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

CENPBD1P
NR_172519.1 non_coding_transcript_exon

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680
Variant links:
Genes affected
CENPBD1P (HGNC:28272): (CENPB DNA-binding domain containing 1, pseudogene) Predicted to enable DNA binding activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.07350215).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CENPBD1PNR_172519.1 linkn.749G>A non_coding_transcript_exon_variant Exon 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CENPBD1PENST00000565150.2 linkn.175G>A non_coding_transcript_exon_variant Exon 1 of 1 5
CENPBD1PENST00000646748.1 linkn.787G>A non_coding_transcript_exon_variant Exon 1 of 1
CENPBD1PENST00000567035.1 linkn.257+181G>A intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1460408
Hom.:
0
Cov.:
34
AF XY:
0.00000413
AC XY:
3
AN XY:
726410
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000360
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.29
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
10
DANN
Benign
0.87
DEOGEN2
Benign
0.00079
T
Eigen
Benign
-0.70
Eigen_PC
Benign
-0.76
FATHMM_MKL
Benign
0.054
N
LIST_S2
Benign
0.67
T
M_CAP
Benign
0.0042
T
MetaRNN
Benign
0.074
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.55
N
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-0.90
N
REVEL
Benign
0.024
Sift
Benign
0.87
T
Sift4G
Benign
0.21
T
Polyphen
0.46
P
Vest4
0.21
MutPred
0.36
Gain of MoRF binding (P = 0.0383);
MVP
0.24
MPC
0.067
ClinPred
0.13
T
GERP RS
2.1
Varity_R
0.082
gMVP
0.10

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-90038156; API