6-42828613-C-G

Variant names:

• chr6-42828613-C-G
• rs1764374902
• NM_001393499.1:c.280C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001393499.1(BICRAL):​c.280C>G​(p.Leu94Val) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L94I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BICRAL NM_001393499.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.24
• Publications: 0 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17996633).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393499.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICRAL	NM_001393499.1	MANE Select	c.280C>G	p.Leu94Val	missense	Exon 6 of 13	NP_001380428.1	Q6AI39
	BICRAL	NM_001318819.2		c.280C>G	p.Leu94Val	missense	Exon 7 of 14	NP_001305748.1	Q6AI39
	BICRAL	NM_015349.3		c.280C>G	p.Leu94Val	missense	Exon 5 of 12	NP_056164.1	Q6AI39

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICRAL	ENST00000314073.10	TSL:1 MANE Select	c.280C>G	p.Leu94Val	missense	Exon 6 of 13	ENSP00000313933.4	Q6AI39
	BICRAL	ENST00000394168.1	TSL:1	c.280C>G	p.Leu94Val	missense	Exon 5 of 12	ENSP00000377723.1	Q6AI39
	BICRAL	ENST00000909955.1		c.280C>G	p.Leu94Val	missense	Exon 5 of 12	ENSP00000580014.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000468 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.021	T
Eigen	Uncertain	0.39
Eigen_PC	Uncertain	0.49
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.87	D
M_CAP	Benign	0.0061	T
MetaRNN	Benign	0.18	T
MetaSVM	Benign	-1.1	T
PhyloP100		4.2
PrimateAI	Benign	0.45	T
PROVEAN	Benign	-0.050	N
REVEL	Benign	0.15
Sift	Benign	0.21	T
Sift4G	Benign	0.44	T
Polyphen		0.89	P
Vest4		0.26
MutPred		0.14		Loss of helix (P = 0.1706)
MVP		0.043
MPC		0.79
ClinPred		0.67	D
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.035
gMVP		0.12
Mutation Taster		=92/8	polymorphism

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: rs1764374902; hg19: chr6-42796351;