chr5-71552856-T-C

Position:

• chr5-71552856-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_018429.3(BDP1):​c.6996-260T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,558 control chromosomes in the GnomAD database, including 15,405 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.45 (15405 hom., cov: 31)
• Consequence: BDP1 NM_018429.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0480

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 5-71552856-T-C is Benign according to our data. Variant chr5-71552856-T-C is described in ClinVar as [Benign]. Clinvar id is 1250427.Status of the report is criteria_provided_single_submitter, 1 stars.
• 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.6996-260T>C		intron_variant		ENST00000358731.9	NP_060899.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDP1	ENST00000358731.9	c.6996-260T>C		intron_variant		1	NM_018429.3	ENSP00000351575.4
BDP1	ENST00000525844.1	n.1062-260T>C		intron_variant		1		ENSP00000432404.1
BDP1	ENST00000514903.7	n.1574-260T>C		intron_variant		5		ENSP00000421910.3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67514 AN: 151442 Hom.: 15404 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.446 AC: 67541 AN: 151558 Hom.: 15405 Cov.: 31 AF XY: 0.448 AC XY: 33152 AN XY: 74058

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.447

Alfa AF: 0.447 Hom.: 1876

Bravo AF: 0.424

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.20

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: rs466930; hg19: chr5-70848683;