19-47675872-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001394372.1(BICRA):​c.106G>A​(p.Asp36Asn) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

BICRA
NM_001394372.1 missense

Scores

2
4
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.08
Variant links:
Genes affected
BICRA (HGNC:4332): (BRD4 interacting chromatin remodeling complex associated protein) Enables transcription regulator activator activity. Involved in positive regulation of transcription, DNA-templated. Located in nucleus. Part of SWI/SNF complex. Implicated in Coffin-Siris syndrome. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.30958182).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BICRANM_001394372.1 linkuse as main transcriptc.106G>A p.Asp36Asn missense_variant 5/15 ENST00000594866.3 NP_001381301.1
BICRANM_015711.3 linkuse as main transcriptc.106G>A p.Asp36Asn missense_variant 5/15 NP_056526.3 Q9NZM4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BICRAENST00000594866.3 linkuse as main transcriptc.106G>A p.Asp36Asn missense_variant 5/152 NM_001394372.1 ENSP00000469738.2 Q9NZM4-1M0QYC3
BICRAENST00000396720.7 linkuse as main transcriptc.106G>A p.Asp36Asn missense_variant 5/155 ENSP00000379946.2 Q9NZM4-1
ENSG00000268746ENST00000599924.1 linkuse as main transcriptn.87-56193G>A intron_variant 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2024BICRA: PM2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.57
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.44
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0037
T;T
Eigen
Uncertain
0.50
Eigen_PC
Uncertain
0.51
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.78
T;T
M_CAP
Benign
0.035
D
MetaRNN
Benign
0.31
T;T
MetaSVM
Benign
-0.41
T
PrimateAI
Uncertain
0.74
T
PROVEAN
Benign
-1.2
N;.
REVEL
Benign
0.21
Sift
Benign
0.15
T;.
Sift4G
Benign
0.078
T;T
Polyphen
1.0
D;.
Vest4
0.43
MutPred
0.21
Gain of catalytic residue at D36 (P = 0.0048);Gain of catalytic residue at D36 (P = 0.0048);
MVP
0.59
MPC
1.1
ClinPred
0.92
D
GERP RS
3.8
Varity_R
0.13
gMVP
0.28

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-48179129; COSMIC: COSV67604718; COSMIC: COSV67604718; API