rs1035938

Positions:

• chr19-47680514-C-G
• chr19-47680514-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001394372.1(BICRA):​c.1344C>G​(p.Ser448Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BICRA NM_001394372.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

Genes affected

BICRA (HGNC:4332): (BRD4 interacting chromatin remodeling complex associated protein) Enables transcription regulator activator activity. Involved in positive regulation of transcription, DNA-templated. Located in nucleus. Part of SWI/SNF complex. Implicated in Coffin-Siris syndrome. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

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/exons	MANE	Protein	UniProt
BICRA	NM_001394372.1	c.1344C>G	p.Ser448Arg	missense_variant	6/15	ENST00000594866.3	NP_001381301.1
BICRA	NM_015711.3	c.1344C>G	p.Ser448Arg	missense_variant	6/15		NP_056526.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BICRA	ENST00000594866.3	c.1344C>G	p.Ser448Arg	missense_variant	6/15	2	NM_001394372.1	ENSP00000469738	P2
	ENST00000599924.1	n.87-51551C>G		intron_variant, non_coding_transcript_variant		5
BICRA	ENST00000396720.7	c.1344C>G	p.Ser448Arg	missense_variant	6/15	5		ENSP00000379946	P2
BICRA	ENST00000614245.2	c.618C>G	p.Ser206Arg	missense_variant	1/10	5		ENSP00000480219	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 42

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.090
CADD	Benign	13
DANN	Benign	0.87
DEOGEN2	Benign	0.064	T;.
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.43
FATHMM_MKL	Benign	0.23	N
LIST_S2	Benign	0.84	T;T
M_CAP	Benign	0.077	D
MetaRNN	Uncertain	0.59	D;D
MetaSVM	Benign	-0.45	T
MutationTaster	Benign	0.87	D
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-2.1	N;.
REVEL	Uncertain	0.33
Sift	Uncertain	0.0010	D;.
Sift4G	Benign	0.061	T;T
Polyphen		1.0	D;.
Vest4		0.77
MutPred		0.35		Loss of loop (P = 0.0022);.;
MVP		0.57
MPC		0.21
ClinPred		0.49	T
GERP RS		-2.1
Varity_R		0.29
gMVP		0.78

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: rs1035938; hg19: chr19-48183771;