dbSNP rs3116068: BRMS1:c.*360G>A (chr11-66337522-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015399.4(BRMS1):c.*360G>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 0.194 in 691,074 control chromosomes in the GnomAD database, including 13,951 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2570 hom., cov: 33)

Exomes 𝑓: 0.20 ( 11381 hom. )

Consequence

BRMS1
NM_015399.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Publications

16 publications found

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]

BRMS1 links:

ENSG00000254756 (HGNC:):

ENSG00000254756 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BRMS1	NM_015399.4 link	c.*360G>A	3_prime_UTR_variant	Exon 10 of 10	ENST00000359957.8	NP_056214.1	Q9HCU9
BRMS1	NM_001024957.2 link	c.*146G>A	3_prime_UTR_variant	Exon 10 of 10		NP_001020128.1	G5E9I4
BRMS1	XM_024448425.2 link	c.*146G>A	3_prime_UTR_variant	Exon 9 of 9		XP_024304193.1
BRMS1	XM_024448426.2 link	c.*112G>A	3_prime_UTR_variant	Exon 9 of 9		XP_024304194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRMS1	ENST00000359957.8 link	c.*360G>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_015399.4	ENSP00000353042.3		Q9HCU9

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25940

AN:

152104

Hom.:

2572

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0829

Gnomad AMI

AF:

0.0989

Gnomad AMR

AF:

0.150

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.271

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.249

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.200

GnomAD4 exome

AF:

0.201

AC:

108244

AN:

538852

Hom.:

11381

Cov.:

AF XY:

0.199

AC XY:

55414

AN XY:

278144

show subpopulations

African (AFR)

AF:

0.0860

AC:

1229

AN:

14294

American (AMR)

AF:

0.129

AC:

2429

AN:

18902

Ashkenazi Jewish (ASJ)

AF:

0.241

AC:

3417

AN:

14164

East Asian (EAS)

AF:

0.247

AC:

7722

AN:

31286

South Asian (SAS)

AF:

0.136

AC:

6264

AN:

46216

European-Finnish (FIN)

AF:

0.245

AC:

7307

AN:

29836

Middle Eastern (MID)

AF:

0.234

AC:

885

AN:

3776

European-Non Finnish (NFE)

AF:

0.209

AC:

73369

AN:

351406

Other (OTH)

AF:

0.194

AC:

5622

AN:

28972

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

4369

8738

13108

17477

21846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.170

AC:

25933

AN:

152222

Hom.:

2570

Cov.:

AF XY:

0.174

AC XY:

12961

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.0827

AC:

3438

AN:

41558

American (AMR)

AF:

0.150

AC:

2289

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

844

AN:

3466

East Asian (EAS)

AF:

0.271

AC:

1404

AN:

5176

South Asian (SAS)

AF:

0.141

AC:

682

AN:

4828

European-Finnish (FIN)

AF:

0.249

AC:

2635

AN:

10592

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.207

AC:

14057

AN:

67996

Other (OTH)

AF:

0.202

AC:

427

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

1104

2207

3311

4414

5518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.201

Hom.:

1087

Bravo

AF:

0.162

Asia WGS

AF:

0.198

AC:

690

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.5

(source)

DANN

Benign

0.48

PhyloP100

-1.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs3116068

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over