5-71461958-C-CT

Position:

• chr5-71461958-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_018429.3(BDP1):​c.599+53dup 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.304

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 -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	UniProt
BDP1	NM_018429.3	c.599+53dup		intron_variant		ENST00000358731.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDP1	ENST00000358731.9	c.599+53dup		intron_variant		1	NM_018429.3	P1
BDP1	ENST00000508917.6	n.791+53dup		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.651 AC: 71137 AN: 109244 Hom.: 25684 Cov.: 0

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.: 57 AF XY: 0.165 AC XY: 4104 AN XY: 24802

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.: 0 AF XY: 0.259 AC XY: 46529 AN XY: 179750

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.: 0 AF XY: 0.645 AC XY: 31995 AN XY: 49594

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs370261571; hg19: chr5-70757785;