6-42829108-A-T

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 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

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 Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICRAL	NM_001393499.1	c.775A>T	p.Thr259Ser	missense_variant	Exon 6 of 13	ENST00000314073.10	NP_001380428.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICRAL	ENST00000314073.10	c.775A>T	p.Thr259Ser	missense_variant	Exon 6 of 13	1	NM_001393499.1	ENSP00000313933.4
BICRAL	ENST00000394168.1	c.775A>T	p.Thr259Ser	missense_variant	Exon 5 of 12	1		ENSP00000377723.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Sep 27, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.775A>T (p.T259S) alteration is located in exon 5 (coding exon 4) of the GLTSCR1L gene. This alteration results from a A to T substitution at nucleotide position 775, causing the threonine (T) at amino acid position 259 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

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;T;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;T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-0.48	.;N;N
REVEL	Benign	0.12
Sift	Benign	0.052	.;T;T
Sift4G	Benign	0.58	T;T;T
Polyphen		0.99	D;D;D
Vest4		0.61
MutPred		0.26		Loss of catalytic residue at T259 (P = 0.0292);Loss of catalytic residue at T259 (P = 0.0292);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

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-42796846;