chr5-71461958-C-CTTTTT

Position:

• chr5-71461958-C-CTTTTT

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_018429.3(BDP1):​c.599+49_599+53dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0040 (5 hom., cov: 0)
  • Exomes 𝑓: 0.00060 (0 hom.)
• Consequence: BDP1 NM_018429.3 intron
• Clinical Significance: Likely 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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 5-71461958-C-CTTTTT is Benign according to our data. Variant chr5-71461958-C-CTTTTT is described in ClinVar as [Likely_benign]. Clinvar id is 1700524.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BDP1	NM_018429.3	c.599+49_599+53dup		intron_variant		ENST00000358731.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDP1	ENST00000358731.9	c.599+49_599+53dup		intron_variant		1	NM_018429.3	P1
BDP1	ENST00000508917.6	n.791+49_791+53dup		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.00404 AC: 441 AN: 109052 Hom.: 5 Cov.: 0

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00124

Gnomad ASJ AF: 0.000328

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000157

Gnomad OTH AF: 0.00211

GnomAD4 exome AF: 0.000603 AC: 202 AN: 334714 Hom.: 0 Cov.: 0 AF XY: 0.000621 AC XY: 114 AN XY: 183564

Gnomad4 AFR exome AF: 0.00353

Gnomad4 AMR exome AF: 0.000446

Gnomad4 ASJ exome AF: 0.000801

Gnomad4 EAS exome AF: 0.000425

Gnomad4 SAS exome AF: 0.00101

Gnomad4 FIN exome AF: 0.0000954

Gnomad4 NFE exome AF: 0.000448

Gnomad4 OTH exome AF: 0.000922

GnomAD4 genome AF: 0.00404 AC: 441 AN: 109036 Hom.: 5 Cov.: 0 AF XY: 0.00426 AC XY: 211 AN XY: 49500

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.00124

Gnomad4 ASJ AF: 0.000328

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000157

Gnomad4 OTH AF: 0.00210

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 07, 2022

See Variant Classification Assertion Criteria. -

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;