chr6-42829108-A-T

Variant names:

• chr6-42829108-A-T
• NM_001393499.1:c.775A>T

Variant summary

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

The NM_001393499.1(BICRAL):​c.775A>T​(p.Thr259Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BICRAL NM_001393499.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.97
• 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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.775A>T	p.Thr259Ser	missense	Exon 6 of 13	NP_001380428.1	Q6AI39
	BICRAL	NM_001318819.2		c.775A>T	p.Thr259Ser	missense	Exon 7 of 14	NP_001305748.1	Q6AI39
	BICRAL	NM_015349.3		c.775A>T	p.Thr259Ser	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.775A>T	p.Thr259Ser	missense	Exon 6 of 13	ENSP00000313933.4	Q6AI39
	BICRAL	ENST00000394168.1	TSL:1	c.775A>T	p.Thr259Ser	missense	Exon 5 of 12	ENSP00000377723.1	Q6AI39
	BICRAL	ENST00000909955.1		c.775A>T	p.Thr259Ser	missense	Exon 5 of 12	ENSP00000580014.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.041	T
BayesDel_noAF	Benign	-0.30
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.012	T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.80	T
M_CAP	Benign	0.012	T
MetaRNN	Uncertain	0.43	T
MetaSVM	Benign	-1.0	T
PhyloP100		6.0
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-0.48	N
REVEL	Benign	0.12
Sift	Benign	0.052	T
Sift4G	Benign	0.58	T
Polyphen		0.99	D
Vest4		0.61
MutPred		0.26		Loss of catalytic residue at T259 (P = 0.0292)
MVP		0.068
MPC		0.73
ClinPred		0.86	D
GERP RS		5.2
Varity_R		0.080
gMVP		0.51
Mutation Taster		=84/16	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

hg19: chr6-42796846;