5-71532590-TTTTGTTTG-TTTTG

Position:

• chr5-71532590-TTTTGTTTG-TTTTG

Variant summary

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

The ENST00000358731.9(BDP1):​c.5892+173_5892+176del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.30 (7825 hom., cov: 19)
• Consequence: BDP1 ENST00000358731.9 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.494

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 5-71532590-TTTTG-T is Benign according to our data. Variant chr5-71532590-TTTTG-T is described in ClinVar as [Benign]. Clinvar id is 1276613.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDP1	NM_018429.3	c.5892+173_5892+176del		intron_variant		ENST00000358731.9	NP_060899.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDP1	ENST00000358731.9	c.5892+173_5892+176del		intron_variant		1	NM_018429.3	ENSP00000351575	P1
BDP1	ENST00000525844.1	c.54+173_54+176del		intron_variant, NMD_transcript_variant		1		ENSP00000432404
BDP1	ENST00000508917.6	n.6084+173_6084+176del		intron_variant, non_coding_transcript_variant		1
BDP1	ENST00000514903.7	c.662+173_662+176del		intron_variant, NMD_transcript_variant		5		ENSP00000421910

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45473 AN: 151774 Hom.: 7819 Cov.: 19

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.394

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.299 AC: 45487 AN: 151894 Hom.: 7825 Cov.: 19 AF XY: 0.301 AC XY: 22341 AN XY: 74202

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.335

Bravo AF: 0.315

Asia WGS AF: 0.363 AC: 1257 AN: 3466

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

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: rs2307799; hg19: chr5-70828417;