20-50795027-G-C

Variant names:

• chr20-50795027-G-C
• rs1274929090
• ENST00000358791.9:c.34G>C

Variant summary

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

The NM_017843.4(BCAS4):​c.34G>C​(p.Gly12Arg) 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. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BCAS4 NM_017843.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288
• Publications: 1 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=0.09579378).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017843.4. 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_017843.4		c.34G>C	p.Gly12Arg	missense	Exon 1 of 6	NP_060313.3	Q8TDM0-1
	BCAS4	NM_001010974.2		c.34G>C	p.Gly12Arg	missense	Exon 1 of 4	NP_001010974.1	Q8TDM0
	BCAS4	NM_198799.4	MANE Select	c.-57G>C		upstream_gene	N/A	NP_942094.3	A0A804CEY2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS4	ENST00000358791.9	TSL:1	c.34G>C	p.Gly12Arg	missense	Exon 1 of 6	ENSP00000351642.5	Q8TDM0-1
	BCAS4	ENST00000912028.1		c.-57G>C		5_prime_UTR	Exon 1 of 5	ENSP00000582087.1
	BCAS4	ENST00000912027.1		c.-57G>C		5_prime_UTR	Exon 1 of 5	ENSP00000582086.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1265042 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 621982

African (AFR) AF: 0.00 AC: 0 AN: 26240

American (AMR) AF: 0.00 AC: 0 AN: 24670

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21498

East Asian (EAS) AF: 0.00 AC: 0 AN: 27926

South Asian (SAS) AF: 0.00 AC: 0 AN: 63716

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32398

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3634

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1013622

Other (OTH) AF: 0.00 AC: 0 AN: 51338

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.49
CADD	Benign	11
DANN	Uncertain	0.98
DEOGEN2	Benign	0.0037	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.0061	N
LIST_S2	Benign	0.60	T
M_CAP	Uncertain	0.12	D
MetaRNN	Benign	0.096	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.4	L
PhyloP100		-0.29
PrimateAI	Uncertain	0.67	T
PROVEAN	Benign	-1.5	N
REVEL	Benign	0.039
Sift	Uncertain	0.0090	D
Sift4G	Uncertain	0.0040	D
Polyphen		0.023	B
Vest4		0.13
MutPred		0.23		Gain of methylation at G12 (P = 0.0141)
MVP		0.24
MPC		0.45
ClinPred		0.13	T
GERP RS		1.6
PromoterAI		-0.024	Neutral
Varity_R		0.082
gMVP		0.066
Mutation Taster		=95/5	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: rs1274929090; hg19: chr20-49411564;