Variant chr5-71539065-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_018429.3(BDP1):c.5916C>A(p.Ile1972=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0272 in 1,599,206 control chromosomes in the GnomAD database, including 791 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.025 ( 73 hom., cov: 32)

Exomes 𝑓: 0.027 ( 718 hom. )

Consequence

BDP1
NM_018429.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.250

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]

BDP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP6

Variant 5-71539065-C-A is Benign according to our data. Variant chr5-71539065-C-A is described in ClinVar as [Benign]. Clinvar id is 508602.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.25 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDP1	NM_018429.3 linkuse as main transcript	c.5916C>A	p.Ile1972=	synonymous_variant	27/39	ENST00000358731.9	NP_060899.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDP1	ENST00000358731.9 linkuse as main transcript	c.5916C>A	p.Ile1972=	synonymous_variant	27/39	1	NM_018429.3	ENSP00000351575	P1	A6H8Y1-1
BDP1	ENST00000508917.6 linkuse as main transcript	n.6108C>A		non_coding_transcript_exon_variant	27/32	1
BDP1	ENST00000525844.1 linkuse as main transcript	c.78C>A	p.Ile26=	synonymous_variant, NMD_transcript_variant	2/14	1		ENSP00000432404
BDP1	ENST00000514903.7 linkuse as main transcript	c.687C>A	p.Ile229=	synonymous_variant, NMD_transcript_variant	4/16	5		ENSP00000421910

Frequencies

GnomAD3 genomes

AF:

0.0250

AC:

3804

AN:

152030

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0115

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0305

Gnomad ASJ

AF:

0.0251

Gnomad EAS

AF:

0.0139

Gnomad SAS

AF:

0.0737

Gnomad FIN

AF:

0.0381

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.0278

Gnomad OTH

AF:

0.0235

GnomAD3 exomes

AF:

0.0321

AC:

7825

AN:

244140

Hom.:

192

AF XY:

0.0336

AC XY:

4452

AN XY:

132604

show subpopulations

Gnomad AFR exome

AF:

0.0106

Gnomad AMR exome

AF:

0.0369

Gnomad ASJ exome

AF:

0.0241

Gnomad EAS exome

AF:

0.0114

Gnomad SAS exome

AF:

0.0640

Gnomad FIN exome

AF:

0.0353

Gnomad NFE exome

AF:

0.0288

Gnomad OTH exome

AF:

0.0266

GnomAD4 exome

AF:

0.0274

AC:

39620

AN:

1447058

Hom.:

718

Cov.:

AF XY:

0.0286

AC XY:

20637

AN XY:

720324

show subpopulations

Gnomad4 AFR exome

AF:

0.00870

Gnomad4 AMR exome

AF:

0.0366

Gnomad4 ASJ exome

AF:

0.0250

Gnomad4 EAS exome

AF:

0.00814

Gnomad4 SAS exome

AF:

0.0650

Gnomad4 FIN exome

AF:

0.0360

Gnomad4 NFE exome

AF:

0.0251

Gnomad4 OTH exome

AF:

0.0256

GnomAD4 genome

AF:

0.0250

AC:

3805

AN:

152148

Hom.:

Cov.:

AF XY:

0.0257

AC XY:

1909

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.0115

Gnomad4 AMR

AF:

0.0305

Gnomad4 ASJ

AF:

0.0251

Gnomad4 EAS

AF:

0.0139

Gnomad4 SAS

AF:

0.0735

Gnomad4 FIN

AF:

0.0381

Gnomad4 NFE

AF:

0.0278

Gnomad4 OTH

AF:

0.0232

Alfa

AF:

0.0257

Hom.:

Bravo

AF:

0.0220

Asia WGS

AF:

0.0410

AC:

141

AN:

3476

EpiCase

AF:

0.0246

EpiControl

AF:

0.0238

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 28, 2017

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.27

CADD

Benign

7.0

DANN

Benign

0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over