Variant 5-71461958-C-CT 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+53dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.65 ( 25661 hom., cov: 0)

Exomes 𝑓: 0.26 ( 161 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-C-CT is Benign according to our data. Variant chr5-71461958-C-CT is described in ClinVar as [Benign]. Clinvar id is 1250600.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDP1	NM_018429.3 link	c.599+53dupT		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+32_599+33insT		intron_variant		1	NM_018429.3	ENSP00000351575.4		A6H8Y1-1
BDP1	ENST00000508917.6 link	n.791+32_791+33insT		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.651

AC:

71137

AN:

109244

Hom.:

25684

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.803

Gnomad AMR

AF:

0.727

Gnomad ASJ

AF:

0.793

Gnomad EAS

AF:

0.822

Gnomad SAS

AF:

0.739

Gnomad FIN

AF:

0.642

Gnomad MID

AF:

0.675

Gnomad NFE

AF:

0.763

Gnomad OTH

AF:

0.709

GnomAD3 exomes

AF:

0.177

AC:

8333

AN:

47180

Hom.:

AF XY:

0.165

AC XY:

4104

AN XY:

24802

show subpopulations

Gnomad AFR exome

AF:

0.137

Gnomad AMR exome

AF:

0.275

Gnomad ASJ exome

AF:

0.237

Gnomad EAS exome

AF:

0.259

Gnomad SAS exome

AF:

0.181

Gnomad FIN exome

AF:

0.0726

Gnomad NFE exome

AF:

0.140

Gnomad OTH exome

AF:

0.228

GnomAD4 exome

AF:

0.261

AC:

85510

AN:

327906

Hom.:

161

Cov.:

AF XY:

0.259

AC XY:

46529

AN XY:

179750

show subpopulations

Gnomad4 AFR exome

AF:

0.171

Gnomad4 AMR exome

AF:

0.245

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.290

Gnomad4 SAS exome

AF:

0.246

Gnomad4 FIN exome

AF:

0.204

Gnomad4 NFE exome

AF:

0.272

Gnomad4 OTH exome

AF:

0.266

GnomAD4 genome

AF:

0.651

AC:

71092

AN:

109228

Hom.:

25661

Cov.:

AF XY:

0.645

AC XY:

31995

AN XY:

49594

show subpopulations

Gnomad4 AFR

AF:

0.353

Gnomad4 AMR

AF:

0.727

Gnomad4 ASJ

AF:

0.793

Gnomad4 EAS

AF:

0.822

Gnomad4 SAS

AF:

0.741

Gnomad4 FIN

AF:

0.642

Gnomad4 NFE

AF:

0.763

Gnomad4 OTH

AF:

0.707

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

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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