Variant 5-71461958-CT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018429.3(BDP1):c.599+53delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.032 ( 26 hom., cov: 0)

Exomes 𝑓: 0.11 ( 3 hom. )

Consequence

BDP1
NM_018429.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.304

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 -10 ACMG points.

BP6

Variant 5-71461958-CT-C is Benign according to our data. Variant chr5-71461958-CT-C is described in ClinVar as [Benign]. Clinvar id is 1245971.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDP1	NM_018429.3 link	c.599+53delT		intron_variant		ENST00000358731.9	NP_060899.2	A6H8Y1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDP1	ENST00000358731.9 link	c.599+33delT		intron_variant		1	NM_018429.3	ENSP00000351575.4		A6H8Y1-1
BDP1	ENST00000508917.6 link	n.791+33delT		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0317

AC:

3449

AN:

108920

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0395

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0328

Gnomad ASJ

AF:

0.0223

Gnomad EAS

AF:

0.0250

Gnomad SAS

AF:

0.0689

Gnomad FIN

AF:

0.0406

Gnomad MID

AF:

0.0244

Gnomad NFE

AF:

0.0266

Gnomad OTH

AF:

0.0267

GnomAD3 exomes

AF:

0.0968

AC:

4568

AN:

47180

Hom.:

AF XY:

0.0930

AC XY:

2306

AN XY:

24802

show subpopulations

Gnomad AFR exome

AF:

0.114

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.113

Gnomad EAS exome

AF:

0.122

Gnomad SAS exome

AF:

0.107

Gnomad FIN exome

AF:

0.0612

Gnomad NFE exome

AF:

0.0742

Gnomad OTH exome

AF:

0.119

GnomAD4 exome

AF:

0.105

AC:

34291

AN:

325108

Hom.:

Cov.:

AF XY:

0.105

AC XY:

18635

AN XY:

178044

show subpopulations

Gnomad4 AFR exome

AF:

0.139

Gnomad4 AMR exome

AF:

0.102

Gnomad4 ASJ exome

AF:

0.0948

Gnomad4 EAS exome

AF:

0.108

Gnomad4 SAS exome

AF:

0.106

Gnomad4 FIN exome

AF:

0.0873

Gnomad4 NFE exome

AF:

0.106

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.0317

AC:

3450

AN:

108904

Hom.:

Cov.:

AF XY:

0.0320

AC XY:

1583

AN XY:

49430

show subpopulations

Gnomad4 AFR

AF:

0.0396

Gnomad4 AMR

AF:

0.0327

Gnomad4 ASJ

AF:

0.0223

Gnomad4 EAS

AF:

0.0251

Gnomad4 SAS

AF:

0.0688

Gnomad4 FIN

AF:

0.0406

Gnomad4 NFE

AF:

0.0266

Gnomad4 OTH

AF:

0.0266

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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