BRMS1 p.Leu67Leu

Variant names:

• chr11-66341561-C-C
• NM_015399.4:c.

Your query was ambiguous. Multiple possible variants found:

• chr11-66341562--
• chr11-66341564-G-A
• chr11-66341562-T-A
• chr11-66341562-T-G
• chr11-66341562-T-C
• chr11-66341562-TAG-CAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015399.4(BRMS1):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRMS1 NM_015399.4 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04
• Publications: 0 publications found

Genes affected

BRMS1 (HGNC:17262): (BRMS1 transcriptional repressor and anoikis regulator) This gene reduces the metastatic potential, but not the tumorogenicity, of human breast cancer and melanoma cell lines. The protein encoded by this gene localizes primarily to the nucleus and is a component of the mSin3a family of histone deacetylase complexes (HDAC). The protein contains two coiled-coil motifs and several imperfect leucine zipper motifs. Alternative splicing results in two transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ENSG00000254756 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015399.4. 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
	BRMS1	NM_015399.4	MANE Select	c.		exon_region	Exon 3 of 10	NP_056214.1	Q9HCU9
	BRMS1	NM_001024957.2		c.		exon_region	Exon 3 of 10	NP_001020128.1	G5E9I4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRMS1	ENST00000359957.8	TSL:1 MANE Select	c.		exon_region	Exon 3 of 10	ENSP00000353042.3	Q9HCU9
	BRMS1	ENST00000530756.1	TSL:1	c.		exon_region	Exon 3 of 9	ENSP00000433740.1	E9PJF5
	BRMS1	ENST00000877326.1		c.		exon_region	Exon 3 of 10	ENSP00000547385.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 41

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.0

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: chr11-66109032;