NM_199191.3:c.935-1122A>G

Variant names:

• chr2-28297216-A-G
• rs10189899
• NM_199191.3:c.935-1122A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199191.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BABAM2	NM_199191.3	MANE Select	c.935-1122A>G		intron	N/A	NP_954661.1
	BABAM2	NM_001329114.2		c.935-1122A>G		intron	N/A	NP_001316043.1
	BABAM2	NM_001329115.2		c.935-1122A>G		intron	N/A	NP_001316044.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BABAM2	ENST00000379624.6	TSL:1 MANE Select	c.935-1122A>G		intron	N/A	ENSP00000368945.1
	BABAM2	ENST00000342045.6	TSL:1	c.935-1122A>G		intron	N/A	ENSP00000339371.2
	BABAM2	ENST00000361704.6	TSL:1	c.935-1122A>G		intron	N/A	ENSP00000354699.2

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

African (AFR) AF: 0.734 AC: 30391 AN: 41432

American (AMR) AF: 0.715 AC: 10920 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2208 AN: 3470

East Asian (EAS) AF: 0.634 AC: 3274 AN: 5160

South Asian (SAS) AF: 0.692 AC: 3328 AN: 4812

European-Finnish (FIN) AF: 0.590 AC: 6225 AN: 10546

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42144 AN: 67954

Other (OTH) AF: 0.708 AC: 1498 AN: 2116

Alfa AF: 0.640 Hom.: 100343

Bravo AF: 0.676

Asia WGS AF: 0.680 AC: 2364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.031
DANN	Benign	0.36
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: rs10189899; hg19: chr2-28520083;