rs3863

chr2-28096267-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199191.3(BABAM2):c.571-33004A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,936 control chromosomes in the GnomAD database, including 7,873 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 0.31 (7873 hom., cov: 31)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

Genes affected

BABAM2 (HGNC:1106): (BRISC and BRCA1 A complex member 2) This gene encodes an anti-apoptotic, death receptor-associated protein that interacts with tumor necrosis factor-receptor-1. The encoded protein acts as an adapter in several protein complexes, including the BRCA1-A complex and the BRISC complex. The BRCA1-A complex possesses ubiquitinase activity and targets sites of double strand DNA breaks, while the BRISC complex exhibits deubiquitinase activity and is involved in mitotic spindle assembly. This gene is upregulated in several types of cancer. [provided by RefSeq, Jun 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BABAM2	NM_199191.3	c.571-33004A>G		intron_variant		ENST00000379624.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BABAM2	ENST00000379624.6	c.571-33004A>G		intron_variant		1	NM_199191.3	P1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47644 AN: 151816 Hom.: 7869 Cov.: 31

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.314 AC: 47663 AN: 151936 Hom.: 7873 Cov.: 31 AF XY: 0.312 AC XY: 23159 AN XY: 74258

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.291

Alfa AF: 0.352 Hom.: 4374

Bravo AF: 0.297

Asia WGS AF: 0.384 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	12
Dann	Benign	0.69

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: rs3863; hg19: chr2-28319134;