chr11-66337699-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015399.4(BRMS1):c.*183C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000395 in 1,598,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000072 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00043 ( 0 hom. )
Consequence
BRMS1
NM_015399.4 3_prime_UTR
NM_015399.4 3_prime_UTR
Scores
17
Clinical Significance
Conservation
PhyloP100: -0.256
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
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.015848368).
BP6
?
Variant 11-66337699-G-A is Benign according to our data. Variant chr11-66337699-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2341367.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRMS1 | NM_015399.4 | c.*183C>T | 3_prime_UTR_variant | 10/10 | ENST00000359957.8 | ||
BRMS1 | XM_024448426.2 | c.802C>T | p.Arg268Ter | stop_gained | 9/9 | ||
BRMS1 | NM_001024957.2 | c.842C>T | p.Ser281Leu | missense_variant | 10/10 | ||
BRMS1 | XM_024448425.2 | c.884C>T | p.Ser295Leu | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRMS1 | ENST00000359957.8 | c.*183C>T | 3_prime_UTR_variant | 10/10 | 1 | NM_015399.4 | P1 | ||
ENST00000526655.1 | n.423+1234G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000894 AC: 20AN: 223732Hom.: 0 AF XY: 0.0000822 AC XY: 10AN XY: 121688
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GnomAD4 exome AF: 0.000429 AC: 620AN: 1446484Hom.: 0 Cov.: 30 AF XY: 0.000412 AC XY: 296AN XY: 718632
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GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74482
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at