NM_198799.4:c.287A>G

Variant names:

• chr20-50841788-A-G
• rs755994429
• NM_198799.4:c.287A>G

Variant summary

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

The NM_198799.4(BCAS4):​c.287A>G​(p.His96Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BCAS4 NM_198799.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0330
• Publications: 0 publications found

Genes affected

BCAS4 (HGNC:14367): (breast carcinoma amplified sequence 4) Predicted to be part of BLOC-1 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=0.073323965).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198799.4. 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
	BCAS4	NM_198799.4	MANE Select	c.287A>G	p.His96Arg	missense	Exon 4 of 5	NP_942094.3	A0A804CEY2
	BCAS4	NM_017843.4		c.377A>G	p.His126Arg	missense	Exon 4 of 6	NP_060313.3	Q8TDM0-1
	BCAS4	NM_001010974.2		c.354+11408A>G		intron	N/A	NP_001010974.1	Q8TDM0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS4	ENST00000371608.8	TSL:1 MANE Select	c.287A>G	p.His96Arg	missense	Exon 4 of 5	ENSP00000360669.3	A0A804CEY2
	BCAS4	ENST00000358791.9	TSL:1	c.377A>G	p.His126Arg	missense	Exon 4 of 6	ENSP00000351642.5	Q8TDM0-1
	BCAS4	ENST00000609336.5	TSL:1	c.287A>G	p.His96Arg	missense	Exon 4 of 6	ENSP00000477167.1	A0A0C4DGS6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

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	0.069
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.33
DANN	Benign	0.27
DEOGEN2	Benign	0.0095	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.36	N
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.0068	T
MetaRNN	Benign	0.073	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.3	L
PhyloP100		0.033
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-2.2	N
REVEL	Benign	0.049
Sift	Benign	0.57	T
Sift4G	Benign	0.21	T
Polyphen		0.0020	B
Vest4		0.094
MutPred		0.61		Gain of MoRF binding (P = 0.0139)
MVP		0.17
MPC		0.30
ClinPred		0.067	T
GERP RS		-0.51
Varity_R		0.043
gMVP		0.37
Mutation Taster		=93/7	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: rs755994429; hg19: chr20-49458325;