chr2-28009220-A-G

Variant names:

• chr2-28009220-A-G
• rs10168171
• NM_199191.3:c.301-16006A>G

Variant summary

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

The NM_001329114.2(BABAM2):​c.301-16006A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 151,890 control chromosomes in the GnomAD database, including 42,579 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 0.74 (42579 hom., cov: 30)
• Consequence: BABAM2 NM_001329114.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001329114.2. 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.301-16006A>G		intron	N/A	NP_954661.1
	BABAM2	NM_001329114.2		c.301-16006A>G		intron	N/A	NP_001316043.1
	BABAM2	NM_001329115.2		c.301-16006A>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.301-16006A>G		intron	N/A	ENSP00000368945.1
	BABAM2	ENST00000342045.6	TSL:1	c.301-16006A>G		intron	N/A	ENSP00000339371.2
	BABAM2	ENST00000361704.6	TSL:1	c.301-16006A>G		intron	N/A	ENSP00000354699.2

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112322 AN: 151770 Hom.: 42568 Cov.: 30

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.740 AC: 112371 AN: 151890 Hom.: 42579 Cov.: 30 AF XY: 0.732 AC XY: 54365 AN XY: 74228

African (AFR) AF: 0.662 AC: 27408 AN: 41400

American (AMR) AF: 0.633 AC: 9665 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2965 AN: 3466

East Asian (EAS) AF: 0.382 AC: 1969 AN: 5154

South Asian (SAS) AF: 0.819 AC: 3934 AN: 4802

European-Finnish (FIN) AF: 0.742 AC: 7843 AN: 10568

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56070 AN: 67930

Other (OTH) AF: 0.762 AC: 1606 AN: 2108

Alfa AF: 0.751 Hom.: 7634

Bravo AF: 0.719

Asia WGS AF: 0.592 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.39
PhyloP100		-1.4
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: rs10168171; hg19: chr2-28232087;