NM_199191.3:c.1088+11589A>C
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_199191.3(BABAM2):c.1088+11589A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,614,178 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 4 hom., cov: 32)
Exomes 𝑓: 0.0036 ( 16 hom. )
Consequence
BABAM2
NM_199191.3 intron
NM_199191.3 intron
Scores
7
Splicing: ADA: 0.00003223
2
Clinical Significance
Conservation
PhyloP100: -0.0320
Genes affected
BABAM2 (HGNC:1106): (BRISC and BRCA1 A complex member 2) This gene encodes an anti-apoptotic, death receptor-associated protein that interacts with tumor necrosis factor-receptor-1. The encoded protein acts as an adapter in several protein complexes, including the BRCA1-A complex and the BRISC complex. The BRCA1-A complex possesses ubiquitinase activity and targets sites of double strand DNA breaks, while the BRISC complex exhibits deubiquitinase activity and is involved in mitotic spindle assembly. This gene is upregulated in several types of cancer. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_addAF=-0.749244).
BP6
Variant 2-28310080-A-C is Benign according to our data. Variant chr2-28310080-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2650777.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 4 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00288 AC: 439AN: 152256Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00283 AC: 711AN: 251424Hom.: 4 AF XY: 0.00275 AC XY: 374AN XY: 135880
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GnomAD4 exome AF: 0.00360 AC: 5264AN: 1461804Hom.: 16 Cov.: 30 AF XY: 0.00364 AC XY: 2644AN XY: 727204
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GnomAD4 genome AF: 0.00288 AC: 439AN: 152374Hom.: 4 Cov.: 32 AF XY: 0.00274 AC XY: 204AN XY: 74516
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
BABAM2: BS2; ENSG00000223522: BS2 -
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
GERP RS
Splicing
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Calibrated prediction
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at