rs10189899

chr2-28297216-A-Gchr2-28297216-A-T

Variant summary

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

The NM_199191.3(BABAM2):c.935-1122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 151,972 control chromosomes in the GnomAD database, including 33,747 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 0.66 (33747 hom., cov: 31)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BABAM2	NM_199191.3	c.935-1122A>G		intron_variant		ENST00000379624.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BABAM2	ENST00000379624.6	c.935-1122A>G		intron_variant		1	NM_199191.3	P1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100716 AN: 151854 Hom.: 33709 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.663 AC: 100812 AN: 151972 Hom.: 33747 Cov.: 31 AF XY: 0.665 AC XY: 49346 AN XY: 74248

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.708

Alfa AF: 0.635 Hom.: 62510

Bravo AF: 0.676

Asia WGS AF: 0.680 AC: 2364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.031
Dann	Benign	0.36

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: rs10189899; hg19: chr2-28520083;