rs7448990

Positions:

• chr5-71458107-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018429.3(BDP1):​c.213-472G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,988 control chromosomes in the GnomAD database, including 16,660 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (16660 hom., cov: 32)
• Consequence: BDP1 NM_018429.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDP1	NM_018429.3	c.213-472G>A		intron_variant		ENST00000358731.9	NP_060899.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDP1	ENST00000358731.9	c.213-472G>A		intron_variant		1	NM_018429.3	ENSP00000351575.4
BDP1	ENST00000508917.6	n.405-472G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70550 AN: 151870 Hom.: 16651 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.459

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.464 AC: 70595 AN: 151988 Hom.: 16660 Cov.: 32 AF XY: 0.466 AC XY: 34597 AN XY: 74278

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.458

Alfa AF: 0.460 Hom.: 3437

Bravo AF: 0.445

Asia WGS AF: 0.449 AC: 1561 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.58

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

Other links and lift over

dbSNP: rs7448990; hg19: chr5-70753934;