rs6020802

chr20-50863762-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS4	NM_198799.4	c.400-12724G>A		intron_variant		ENST00000371608.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS4	ENST00000371608.8	c.400-12724G>A		intron_variant		1	NM_198799.4	P2

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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0782

Gnomad4 NFE AF: 0.0951

Gnomad4 OTH AF: 0.138

Alfa AF: 0.112 Hom.: 787

Bravo AF: 0.163

Asia WGS AF: 0.150 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.42
Dann	Benign	0.57

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: rs6020802; hg19: chr20-49480299;