6-42763377-C-T

Variant names:

• chr6-42763377-C-T
• rs6458307
• NM_001318819.2:c.-365+16354C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001318819.2(BICRAL):​c.-365+16354C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,032 control chromosomes in the GnomAD database, including 10,500 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 0.36 (10500 hom., cov: 32)
• Consequence: BICRAL NM_001318819.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318819.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICRAL	NM_001318819.2		c.-365+16354C>T		intron	N/A	NP_001305748.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54374 AN: 151912 Hom.: 10460 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.345

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.358 AC: 54473 AN: 152032 Hom.: 10500 Cov.: 32 AF XY: 0.356 AC XY: 26433 AN XY: 74314

African (AFR) AF: 0.505 AC: 20915 AN: 41448

American (AMR) AF: 0.352 AC: 5376 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1237 AN: 5180

South Asian (SAS) AF: 0.316 AC: 1525 AN: 4828

European-Finnish (FIN) AF: 0.285 AC: 3008 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20437 AN: 67952

Other (OTH) AF: 0.351 AC: 742 AN: 2114

Alfa AF: 0.322 Hom.: 35294

Bravo AF: 0.372

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.38
PhyloP100		-0.58

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

Other links and lift over

dbSNP: rs6458307; hg19: chr6-42731115;