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GeneBe

11-66340784-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_015399.4(BRMS1):c.525C>T(p.Asp175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00278 in 1,611,942 control chromosomes in the GnomAD database, including 126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 65 hom., cov: 32)
Exomes 𝑓: 0.0015 ( 61 hom. )

Consequence

BRMS1
NM_015399.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.57
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 Benign. Variant got -13 ACMG points.

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=-0.32).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-66340784-G-A is Benign according to our data. Variant chr11-66340784-G-A is described in ClinVar as [Benign]. Clinvar id is 776630.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=3.57 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0504 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BRMS1NM_015399.4 linkuse as main transcriptc.525C>T p.Asp175= synonymous_variant 6/10 ENST00000359957.8
BRMS1NM_001024957.2 linkuse as main transcriptc.525C>T p.Asp175= synonymous_variant 6/10
BRMS1XM_024448425.2 linkuse as main transcriptc.525C>T p.Asp175= synonymous_variant 6/9
BRMS1XM_024448426.2 linkuse as main transcriptc.525C>T p.Asp175= synonymous_variant 6/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BRMS1ENST00000359957.8 linkuse as main transcriptc.525C>T p.Asp175= synonymous_variant 6/101 NM_015399.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0148
AC:
2259
AN:
152172
Hom.:
65
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0523
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00412
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.0124
GnomAD3 exomes
AF:
0.00376
AC:
935
AN:
248638
Hom.:
17
AF XY:
0.00268
AC XY:
362
AN XY:
134826
show subpopulations
Gnomad AFR exome
AF:
0.0510
Gnomad AMR exome
AF:
0.00302
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000656
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000623
Gnomad OTH exome
AF:
0.00132
GnomAD4 exome
AF:
0.00152
AC:
2220
AN:
1459652
Hom.:
61
Cov.:
34
AF XY:
0.00127
AC XY:
924
AN XY:
726160
show subpopulations
Gnomad4 AFR exome
AF:
0.0554
Gnomad4 AMR exome
AF:
0.00304
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000163
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000333
Gnomad4 OTH exome
AF:
0.00289
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0149
AC:
2264
AN:
152290
Hom.:
65
Cov.:
32
AF XY:
0.0147
AC XY:
1098
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.0523
Gnomad4 AMR
AF:
0.00405
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.0123
Alfa
AF:
0.00844
Hom.:
21
Bravo
AF:
0.0160
Asia WGS
AF:
0.00404
AC:
14
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000178

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
-0.32
Cadd
Benign
12
Dann
Benign
0.91
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs17850564; hg19: chr11-66108255; API