chr5-71461958-C-CTT

Position:

• chr5-71461958-C-CTT

Variant summary

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

The NM_018429.3(BDP1):​c.599+52_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 0.037 (151 hom., cov: 0)
  • Exomes 𝑓: 0.084 (6 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-CTT is Benign according to our data. Variant chr5-71461958-C-CTT is described in ClinVar as [Benign]. Clinvar id is 1294001.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BDP1	NM_018429.3	c.599+52_599+53dup		intron_variant		ENST00000358731.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDP1	ENST00000358731.9	c.599+52_599+53dup		intron_variant		1	NM_018429.3	P1
BDP1	ENST00000508917.6	n.791+52_791+53dup		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0374 AC: 4071 AN: 108832 Hom.: 151 Cov.: 0

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.0251

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0529

Gnomad EAS AF: 0.0261

Gnomad SAS AF: 0.0268

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0671

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0289

GnomAD3 exomes AF: 0.0679 AC: 3205 AN: 47180 Hom.: 15 AF XY: 0.0645 AC XY: 1599 AN XY: 24802

Gnomad AFR exome AF: 0.0566

Gnomad AMR exome AF: 0.108

Gnomad ASJ exome AF: 0.0805

Gnomad EAS exome AF: 0.0953

Gnomad SAS exome AF: 0.0745

Gnomad FIN exome AF: 0.0207

Gnomad NFE exome AF: 0.0543

Gnomad OTH exome AF: 0.0850

GnomAD4 exome AF: 0.0838 AC: 27005 AN: 322170 Hom.: 6 Cov.: 0 AF XY: 0.0838 AC XY: 14792 AN XY: 176416

Gnomad4 AFR exome AF: 0.0625

Gnomad4 AMR exome AF: 0.0966

Gnomad4 ASJ exome AF: 0.0926

Gnomad4 EAS exome AF: 0.0834

Gnomad4 SAS exome AF: 0.0994

Gnomad4 FIN exome AF: 0.0599

Gnomad4 NFE exome AF: 0.0825

Gnomad4 OTH exome AF: 0.0867

GnomAD4 genome AF: 0.0374 AC: 4069 AN: 108816 Hom.: 151 Cov.: 0 AF XY: 0.0370 AC XY: 1828 AN XY: 49402

Gnomad4 AFR AF: 0.0528

Gnomad4 AMR AF: 0.0437

Gnomad4 ASJ AF: 0.0529

Gnomad4 EAS AF: 0.0263

Gnomad4 SAS AF: 0.0267

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0307

Gnomad4 OTH AF: 0.0281

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

Sep 17, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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;