Genetic Variant BDP1:c.599+50_599+53dupTTTT (chr5-71461958-C-CTTTT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_018429.3(BDP1):c.599+50_599+53dupTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00063 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0030 ( 1 hom. )

Consequence

BDP1
NM_018429.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDP1	NM_018429.3 link	c.599+50_599+53dupTTTT		intron_variant	Intron 3 of 38	ENST00000358731.9	NP_060899.2	A6H8Y1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDP1	ENST00000358731.9 link	c.599+32_599+33insTTTT		intron_variant	Intron 3 of 38	1	NM_018429.3	ENSP00000351575.4		A6H8Y1-1
BDP1	ENST00000508917.6 link	n.791+32_791+33insTTTT		intron_variant	Intron 3 of 31	1

Frequencies

GnomAD3 genomes

AF:

0.000633

AC:

AN:

109042

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000658

Gnomad AMI

AF:

0.00119

Gnomad AMR

AF:

0.000990

Gnomad ASJ

AF:

0.000984

Gnomad EAS

AF:

0.000266

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000441

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000628

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00298

AC:

994

AN:

333658

Hom.:

Cov.:

AF XY:

0.00286

AC XY:

523

AN XY:

182982

show subpopulations

Gnomad4 AFR exome

AF:

0.00402

Gnomad4 AMR exome

AF:

0.00345

Gnomad4 ASJ exome

AF:

0.00345

Gnomad4 EAS exome

AF:

0.00231

Gnomad4 SAS exome

AF:

0.00449

Gnomad4 FIN exome

AF:

0.00177

Gnomad4 NFE exome

AF:

0.00276

Gnomad4 OTH exome

AF:

0.00278

GnomAD4 genome

AF:

0.000633

AC:

AN:

109026

Hom.:

Cov.:

AF XY:

0.000768

AC XY:

AN XY:

49490

show subpopulations

Gnomad4 AFR

AF:

0.000658

Gnomad4 AMR

AF:

0.000990

Gnomad4 ASJ

AF:

0.000984

Gnomad4 EAS

AF:

0.000267

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000441

Gnomad4 NFE

AF:

0.000628

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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.

5-71461958-CTTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over