Variant 19-47680514-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001394372.1(BICRA):c.1344C>T(p.Ser448=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 1,542,428 control chromosomes in the GnomAD database, including 61,620 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 0.32 ( 7988 hom., cov: 32)

Exomes 𝑓: 0.27 ( 53632 hom. )

Consequence

BICRA
NM_001394372.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.840

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 Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP7

Synonymous conserved (PhyloP=-0.84 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICRA	NM_001394372.1 linkuse as main transcript	c.1344C>T	p.Ser448=	synonymous_variant	6/15	ENST00000594866.3
BICRA	NM_015711.3 linkuse as main transcript	c.1344C>T	p.Ser448=	synonymous_variant	6/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICRA	ENST00000594866.3 linkuse as main transcript	c.1344C>T	p.Ser448=	synonymous_variant	6/15	2	NM_001394372.1	P2	Q9NZM4-1
	ENST00000599924.1 linkuse as main transcript	n.87-51551C>T		intron_variant, non_coding_transcript_variant		5
BICRA	ENST00000396720.7 linkuse as main transcript	c.1344C>T	p.Ser448=	synonymous_variant	6/15	5		P2	Q9NZM4-1
BICRA	ENST00000614245.2 linkuse as main transcript	c.618C>T	p.Ser206=	synonymous_variant	1/10	5		A2	Q9NZM4-2

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

47933

AN:

151748

Hom.:

7976

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.296

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.323

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.289

GnomAD3 exomes

AF:

0.290

AC:

41526

AN:

143058

Hom.:

6247

AF XY:

0.291

AC XY:

22482

AN XY:

77154

show subpopulations

Gnomad AFR exome

AF:

0.427

Gnomad AMR exome

AF:

0.288

Gnomad ASJ exome

AF:

0.311

Gnomad EAS exome

AF:

0.290

Gnomad SAS exome

AF:

0.327

Gnomad FIN exome

AF:

0.214

Gnomad NFE exome

AF:

0.271

Gnomad OTH exome

AF:

0.283

GnomAD4 exome

AF:

0.275

AC:

381808

AN:

1390562

Hom.:

53632

Cov.:

AF XY:

0.276

AC XY:

189294

AN XY:

685658

show subpopulations

Gnomad4 AFR exome

AF:

0.439

Gnomad4 AMR exome

AF:

0.292

Gnomad4 ASJ exome

AF:

0.314

Gnomad4 EAS exome

AF:

0.291

Gnomad4 SAS exome

AF:

0.327

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.265

Gnomad4 OTH exome

AF:

0.289

GnomAD4 genome

AF:

0.316

AC:

47993

AN:

151866

Hom.:

7988

Cov.:

AF XY:

0.314

AC XY:

23302

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.430

Gnomad4 AMR

AF:

0.297

Gnomad4 ASJ

AF:

0.304

Gnomad4 EAS

AF:

0.292

Gnomad4 SAS

AF:

0.322

Gnomad4 FIN

AF:

0.222

Gnomad4 NFE

AF:

0.268

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.276

Hom.:

5420

Bravo

AF:

0.324

Asia WGS

AF:

0.351

AC:

1223

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

4.4

DANN

Benign

0.84

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over