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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1

The NM_018429.3(BDP1):c.599+51_599+53delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 437,266 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000055 ( 0 hom., cov: 0)

Exomes 𝑓: 0.019 ( 0 hom. )

Consequence

BDP1
NM_018429.3 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.23

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 Likely_benign. Variant got -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 5-71461958-CTTT-C is Benign according to our data. Variant chr5-71461958-CTTT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1317595.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.0193 (6324/328204) while in subpopulation AFR AF= 0.0268 (224/8350). AF 95% confidence interval is 0.0239. There are 0 homozygotes in gnomad4_exome. There are 3395 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDP1	NM_018429.3 link	c.599+51_599+53delTTT		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+33_599+35delTTT		intron_variant		1	NM_018429.3	ENSP00000351575.4		A6H8Y1-1
BDP1	ENST00000508917.6 link	n.791+33_791+35delTTT		intron_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0000550

AC:

AN:

109062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000104

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000304

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000349

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0181

AC:

855

AN:

47180

Hom.:

AF XY:

0.0172

AC XY:

426

AN XY:

24802

show subpopulations

Gnomad AFR exome

AF:

0.0221

Gnomad AMR exome

AF:

0.0239

Gnomad ASJ exome

AF:

0.0192

Gnomad EAS exome

AF:

0.0212

Gnomad SAS exome

AF:

0.0222

Gnomad FIN exome

AF:

0.0158

Gnomad NFE exome

AF:

0.0145

Gnomad OTH exome

AF:

0.0145

GnomAD4 exome

AF:

0.0193

AC:

6324

AN:

328204

Hom.:

AF XY:

0.0189

AC XY:

3395

AN XY:

179914

show subpopulations

Gnomad4 AFR exome

AF:

0.0268

Gnomad4 AMR exome

AF:

0.0211

Gnomad4 ASJ exome

AF:

0.0194

Gnomad4 EAS exome

AF:

0.0207

Gnomad4 SAS exome

AF:

0.0168

Gnomad4 FIN exome

AF:

0.0156

Gnomad4 NFE exome

AF:

0.0194

Gnomad4 OTH exome

AF:

0.0207

GnomAD4 genome

AF:

0.0000550

AC:

AN:

109062

Hom.:

Cov.:

AF XY:

0.0000404

AC XY:

AN XY:

49492

show subpopulations

Gnomad4 AFR

AF:

0.000104

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000304

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000349

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely 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