Variant 19-47675868-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_001394372.1(BICRA):c.102C>T(p.Leu34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00357 in 1,608,042 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0034 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0036 ( 15 hom. )

Consequence

BICRA
NM_001394372.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.41

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BP6

Variant 19-47675868-C-T is Benign according to our data. Variant chr19-47675868-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1335354.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.41 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00337 (513/152308) while in subpopulation NFE AF= 0.00381 (259/68028). AF 95% confidence interval is 0.00343. There are 3 homozygotes in gnomad4. There are 287 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 513 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BICRA	NM_001394372.1 linkuse as main transcript	c.102C>T	p.Leu34=	synonymous_variant	5/15	ENST00000594866.3	NP_001381301.1
BICRA	NM_015711.3 linkuse as main transcript	c.102C>T	p.Leu34=	synonymous_variant	5/15		NP_056526.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BICRA	ENST00000594866.3 linkuse as main transcript	c.102C>T	p.Leu34=	synonymous_variant	5/15	2	NM_001394372.1	ENSP00000469738	P2	Q9NZM4-1
	ENST00000599924.1 linkuse as main transcript	n.87-56197C>T		intron_variant, non_coding_transcript_variant		5
BICRA	ENST00000396720.7 linkuse as main transcript	c.102C>T	p.Leu34=	synonymous_variant	5/15	5		ENSP00000379946	P2	Q9NZM4-1

Frequencies

GnomAD3 genomes

AF:

0.00337

AC:

513

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000531

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00294

Gnomad ASJ

AF:

0.0135

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.0121

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00381

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00354

AC:

843

AN:

237890

Hom.:

AF XY:

0.00339

AC XY:

438

AN XY:

129372

show subpopulations

Gnomad AFR exome

AF:

0.000554

Gnomad AMR exome

AF:

0.00241

Gnomad ASJ exome

AF:

0.0132

Gnomad EAS exome

AF:

0.000114

Gnomad SAS exome

AF:

0.000339

Gnomad FIN exome

AF:

0.0106

Gnomad NFE exome

AF:

0.00350

Gnomad OTH exome

AF:

0.00395

GnomAD4 exome

AF:

0.00359

AC:

5225

AN:

1455734

Hom.:

Cov.:

AF XY:

0.00347

AC XY:

2511

AN XY:

723640

show subpopulations

Gnomad4 AFR exome

AF:

0.000299

Gnomad4 AMR exome

AF:

0.00263

Gnomad4 ASJ exome

AF:

0.0129

Gnomad4 EAS exome

AF:

0.0000506

Gnomad4 SAS exome

AF:

0.000352

Gnomad4 FIN exome

AF:

0.00877

Gnomad4 NFE exome

AF:

0.00366

Gnomad4 OTH exome

AF:

0.00342

GnomAD4 genome

AF:

0.00337

AC:

513

AN:

152308

Hom.:

Cov.:

AF XY:

0.00385

AC XY:

287

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.000529

Gnomad4 AMR

AF:

0.00294

Gnomad4 ASJ

AF:

0.0135

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.0121

Gnomad4 NFE

AF:

0.00381

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00416

Hom.:

Bravo

AF:

0.00280

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2024	BICRA: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over