1-91992285-CCG-TTA

Variant names:

• chr1-91992285-CCG-TTA
• NM_207189.4:c.2086_2088delCCGinsTTA
• BRDT p.Pro696Leu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_207189.4(BRDT):​c.2086_2088delCCGinsTTA​(p.Pro696Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 29)
• Consequence: BRDT NM_207189.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269
• Publications: 0 publications found

Genes affected

BRDT (HGNC:1105): (bromodomain testis associated) BRDT is similar to the RING3 protein family. It possesses 2 bromodomain motifs and a PEST sequence (a cluster of proline, glutamic acid, serine, and threonine residues), characteristic of proteins that undergo rapid intracellular degradation. The bromodomain is found in proteins that regulate transcription. Several transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

BRDT Gene-Disease associations (from GenCC):

• spermatogenic failure 21

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207189.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRDT	NM_207189.4	MANE Select	c.2086_2088delCCGinsTTA	p.Pro696Leu	missense	N/A	NP_997072.2	Q58F21-1
	BRDT	NM_001242806.2		c.2098_2100delCCGinsTTA	p.Pro700Leu	missense	N/A	NP_001229735.2	Q58F21-3
	BRDT	NM_001242805.2		c.2086_2088delCCGinsTTA	p.Pro696Leu	missense	N/A	NP_001229734.2	Q58F21-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRDT	ENST00000399546.7	TSL:2 MANE Select	c.2086_2088delCCGinsTTA	p.Pro696Leu	missense	N/A	ENSP00000387822.3	Q58F21-1
	BRDT	ENST00000362005.7	TSL:1	c.2086_2088delCCGinsTTA	p.Pro696Leu	missense	N/A	ENSP00000354568.3	Q58F21-1
	BRDT	ENST00000402388.1	TSL:1	c.2086_2088delCCGinsTTA	p.Pro696Leu	missense	N/A	ENSP00000384051.1	Q58F21-1

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-92457842;