chr20-50863762-G-A

Variant names:

• chr20-50863762-G-A
• rs6020802
• NM_198799.4:c.400-12724G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198799.4(BCAS4):​c.400-12724G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,158 control chromosomes in the GnomAD database, including 2,372 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2372 hom., cov: 31)
• Consequence: BCAS4 NM_198799.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

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.400-12724G>A		intron	N/A	NP_942094.3	A0A804CEY2
	BCAS4	NM_017843.4		c.490-12235G>A		intron	N/A	NP_060313.3	Q8TDM0-1
	BCAS4	NM_001010974.2		c.355-12724G>A		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.400-12724G>A		intron	N/A	ENSP00000360669.3	A0A804CEY2
	BCAS4	ENST00000358791.9	TSL:1	c.490-12235G>A		intron	N/A	ENSP00000351642.5	Q8TDM0-1
	BCAS4	ENST00000609336.5	TSL:1	c.400-12235G>A		intron	N/A	ENSP00000477167.1	A0A0C4DGS6

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23299 AN: 152038 Hom.: 2350 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.138

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.154 AC: 23372 AN: 152158 Hom.: 2372 Cov.: 31 AF XY: 0.151 AC XY: 11241 AN XY: 74406

African (AFR) AF: 0.294 AC: 12186 AN: 41484

American (AMR) AF: 0.119 AC: 1821 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3468

East Asian (EAS) AF: 0.103 AC: 530 AN: 5168

South Asian (SAS) AF: 0.107 AC: 518 AN: 4828

European-Finnish (FIN) AF: 0.0782 AC: 829 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6466 AN: 67996

Other (OTH) AF: 0.138 AC: 292 AN: 2114

Alfa AF: 0.114 Hom.: 971

Bravo AF: 0.163

Asia WGS AF: 0.150 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.42
DANN	Benign	0.57
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs6020802; hg19: chr20-49480299;