chr5-71510822-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_018429.3(BDP1):ā€‹c.3730T>Gā€‹(p.Phe1244Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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: 33)
Exomes š‘“: 6.8e-7 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

BDP1
NM_018429.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710
Variant links:
Genes affected
BDP1 (HGNC:13652): (B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB) The product of this gene is a subunit of the TFIIIB transcription initiation complex, which recruits RNA polymerase III to target promoters in order to initiate transcription. The encoded protein localizes to concentrated aggregates in the nucleus, and is required for transcription from all three types of polymerase III promoters. It is phosphorylated by casein kinase II during mitosis, resulting in its release from chromatin and suppression of polymerase III transcription. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.03520882).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BDP1NM_018429.3 linkc.3730T>G p.Phe1244Val missense_variant Exon 17 of 39 ENST00000358731.9 NP_060899.2 A6H8Y1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BDP1ENST00000358731.9 linkc.3730T>G p.Phe1244Val missense_variant Exon 17 of 39 1 NM_018429.3 ENSP00000351575.4 A6H8Y1-1
BDP1ENST00000508917.6 linkn.3922T>G non_coding_transcript_exon_variant Exon 17 of 32 1
BDP1ENST00000508157.3 linkn.2875T>G non_coding_transcript_exon_variant Exon 6 of 6 5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000403
AC:
1
AN:
248262
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
134814
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000464
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
6.84e-7
AC:
1
AN:
1461202
Hom.:
0
Cov.:
52
AF XY:
0.00
AC XY:
0
AN XY:
726982
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:
0.0000187
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
ExAC
AF:
0.00000828
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.062
BayesDel_addAF
Benign
-0.43
T
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.37
DANN
Benign
0.51
DEOGEN2
Benign
0.0032
T
Eigen
Benign
-1.7
Eigen_PC
Benign
-1.7
FATHMM_MKL
Benign
0.0020
N
LIST_S2
Benign
0.13
T
M_CAP
Benign
0.0020
T
MetaRNN
Benign
0.035
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
-0.69
N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
0.95
N
REVEL
Benign
0.0030
Sift
Benign
0.46
T
Sift4G
Benign
0.42
T
Polyphen
0.0
B
Vest4
0.040
MutPred
0.29
Gain of MoRF binding (P = 0.1743);
MVP
0.040
MPC
0.044
ClinPred
0.043
T
GERP RS
-4.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.025
gMVP
0.026

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

LitVar

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

Other links and lift over

dbSNP: rs1961760; hg19: chr5-70806649; API