rs3745760

Positions:

• chr19-47702468-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394372.1(BICRA):​c.*53T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,412,996 control chromosomes in the GnomAD database, including 55,108 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 0.34 (9963 hom., cov: 32)
  • Exomes 𝑓: 0.26 (45145 hom.)
• Consequence: BICRA NM_001394372.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BICRA	NM_001394372.1	c.*53T>C		3_prime_UTR_variant	15/15	ENST00000594866.3	NP_001381301.1
BICRA	NM_015711.3	c.*53T>C		3_prime_UTR_variant	15/15		NP_056526.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BICRA	ENST00000594866.3	c.*53T>C		3_prime_UTR_variant	15/15	2	NM_001394372.1	ENSP00000469738	P2
	ENST00000599924.1	n.87-29597T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51475 AN: 151908 Hom.: 9933 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.262 AC: 330099 AN: 1260972 Hom.: 45145 Cov.: 31 AF XY: 0.263 AC XY: 161581 AN XY: 614840

Gnomad4 AFR exome AF: 0.555

Gnomad4 AMR exome AF: 0.294

Gnomad4 ASJ exome AF: 0.266

Gnomad4 EAS exome AF: 0.310

Gnomad4 SAS exome AF: 0.319

Gnomad4 FIN exome AF: 0.243

Gnomad4 NFE exome AF: 0.249

Gnomad4 OTH exome AF: 0.281

GnomAD4 genome AF: 0.339 AC: 51553 AN: 152024 Hom.: 9963 Cov.: 32 AF XY: 0.337 AC XY: 25065 AN XY: 74294

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.299

Alfa AF: 0.264 Hom.: 8896

Bravo AF: 0.352

Asia WGS AF: 0.358 AC: 1249 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.61

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

Other links and lift over

dbSNP: rs3745760; hg19: chr19-48205725;