6-42867749-C-T

Position:

• chr6-42867749-C-T

Variant summary

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

The NM_001393499.1(BICRAL):​c.*2303C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,096 control chromosomes in the GnomAD database, including 5,362 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 0.20 (5362 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BICRAL NM_001393499.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

BICRAL (HGNC:21111): (BICRA like chromatin remodeling complex associated protein) Predicted to be involved in positive regulation of transcription, DNA-templated. Part of SWI/SNF complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICRAL	NM_001393499.1	c.*2303C>T		3_prime_UTR_variant	13/13	ENST00000314073.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICRAL	ENST00000314073.10	c.*2303C>T		3_prime_UTR_variant	13/13	1	NM_001393499.1	P1
BICRAL	ENST00000394168.1	c.*2303C>T		3_prime_UTR_variant	12/12	1		P1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30006 AN: 151978 Hom.: 5347 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0762

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.168

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.198 AC: 30074 AN: 152096 Hom.: 5362 Cov.: 32 AF XY: 0.196 AC XY: 14582 AN XY: 74364

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.0762

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.174

Alfa AF: 0.103 Hom.: 1600

Bravo AF: 0.214

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.63

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: rs7764865; hg19: chr6-42835487;