Variant 19-47679342-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001394372.1(BICRA):c.172G>T(p.Gly58Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000157 in 1,271,196 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 Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000016 ( 0 hom. )

Consequence

BICRA
NM_001394372.1 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.86

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]

BICRA links:

(HGNC:):

links:

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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=0.32502693).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BICRA	NM_001394372.1 linkuse as main transcript	c.172G>T	p.Gly58Cys	missense_variant	6/15	ENST00000594866.3	NP_001381301.1
BICRA	NM_015711.3 linkuse as main transcript	c.172G>T	p.Gly58Cys	missense_variant	6/15		NP_056526.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BICRA	ENST00000594866.3 linkuse as main transcript	c.172G>T	p.Gly58Cys	missense_variant	6/15	2	NM_001394372.1	ENSP00000469738	P2	Q9NZM4-1
	ENST00000599924.1 linkuse as main transcript	n.87-52723G>T		intron_variant, non_coding_transcript_variant		5
BICRA	ENST00000396720.7 linkuse as main transcript	c.172G>T	p.Gly58Cys	missense_variant	6/15	5		ENSP00000379946	P2	Q9NZM4-1
BICRA	ENST00000614245.2 linkuse as main transcript	c.-555G>T		5_prime_UTR_variant	1/10	5		ENSP00000480219	A2	Q9NZM4-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000157

AC:

AN:

1271196

Hom.:

Cov.:

AF XY:

0.00000163

AC XY:

AN XY:

614590

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.81e-7

Gnomad4 OTH exome

AF:

0.0000191

GnomAD4 genome

Cov.:

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 submitter

clinical testing

GeneDx

Mar 06, 2024

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Uncertain

0.036

BayesDel_noAF

Benign

-0.19

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.065

T;T;.

Eigen

Uncertain

0.38

Eigen_PC

Uncertain

0.37

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.75

T;T;T

M_CAP

Uncertain

0.21

MetaRNN

Benign

0.33

T;T;T

MetaSVM

Uncertain

-0.11

MutationTaster

Benign

0.64

PrimateAI

Uncertain

0.78

PROVEAN

Uncertain

-3.0

D;.;.

REVEL

Benign

0.27

Sift

Uncertain

0.0030

D;.;.

Sift4G

Uncertain

0.019

D;D;D

Polyphen

0.99

D;.;.

Vest4

0.50

MutPred

0.17

Loss of glycosylation at S57 (P = 0.0497);Loss of glycosylation at S57 (P = 0.0497);.;

MVP

0.39

MPC

1.2

ClinPred

0.61

GERP RS

3.9

Varity_R

0.27

gMVP

0.27

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over