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GeneBe

11-66337677-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_015399.4(BRMS1):c.*205G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000251 in 1,571,706 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 0 hom. )

Consequence

BRMS1
NM_015399.4 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0470
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
?
    PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-66337677-C-T is Benign according to our data. Variant chr11-66337677-C-T is described in ClinVar as [Benign]. Clinvar id is 707893.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BRMS1NM_015399.4 linkuse as main transcriptc.*205G>A 3_prime_UTR_variant 10/10 ENST00000359957.8
BRMS1XM_024448426.2 linkuse as main transcriptc.824G>A p.Arg275His missense_variant 9/9
BRMS1NM_001024957.2 linkuse as main transcriptc.864G>A p.Pro288= synonymous_variant 10/10
BRMS1XM_024448425.2 linkuse as main transcriptc.906G>A p.Pro302= synonymous_variant 9/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BRMS1ENST00000359957.8 linkuse as main transcriptc.*205G>A 3_prime_UTR_variant 10/101 NM_015399.4 P1
ENST00000526655.1 linkuse as main transcriptn.423+1212C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00133
AC:
202
AN:
152218
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00465
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000393
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.000957
GnomAD3 exomes
AF:
0.000310
AC:
58
AN:
187254
Hom.:
0
AF XY:
0.000238
AC XY:
24
AN XY:
101022
show subpopulations
Gnomad AFR exome
AF:
0.00464
Gnomad AMR exome
AF:
0.000186
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000387
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000203
GnomAD4 exome
AF:
0.000135
AC:
192
AN:
1419370
Hom.:
0
Cov.:
30
AF XY:
0.000122
AC XY:
86
AN XY:
702604
show subpopulations
Gnomad4 AFR exome
AF:
0.00433
Gnomad4 AMR exome
AF:
0.000239
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000268
Gnomad4 SAS exome
AF:
0.0000487
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000211
Gnomad4 OTH exome
AF:
0.000238
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00133
AC:
203
AN:
152336
Hom.:
1
Cov.:
33
AF XY:
0.00130
AC XY:
97
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.00467
Gnomad4 AMR
AF:
0.000392
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.000947
Alfa
AF:
0.00117
Hom.:
0
Bravo
AF:
0.00139
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeFeb 26, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
Cadd
Benign
6.5
Dann
Benign
0.85
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs370037659; hg19: chr11-66105148; API