rs10173528

Variant names:

• chr2-28065525-C-T
• rs10173528
• NM_199191.3:c.570+19726C>T

Variant summary

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

The NM_199191.3(BABAM2):​c.570+19726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,970 control chromosomes in the GnomAD database, including 20,466 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 0.51 (20466 hom., cov: 31)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.526
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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.570+19726C>T		intron	N/A	NP_954661.1
	BABAM2	NM_001329114.2		c.570+19726C>T		intron	N/A	NP_001316043.1
	BABAM2	NM_001329115.2		c.570+19726C>T		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.570+19726C>T		intron	N/A	ENSP00000368945.1
	BABAM2	ENST00000342045.6	TSL:1	c.570+19726C>T		intron	N/A	ENSP00000339371.2
	BABAM2	ENST00000361704.6	TSL:1	c.570+19726C>T		intron	N/A	ENSP00000354699.2

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77376 AN: 151850 Hom.: 20460 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.509 AC: 77400 AN: 151970 Hom.: 20466 Cov.: 31 AF XY: 0.500 AC XY: 37160 AN XY: 74286

African (AFR) AF: 0.432 AC: 17906 AN: 41444

American (AMR) AF: 0.416 AC: 6352 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1823 AN: 3466

East Asian (EAS) AF: 0.226 AC: 1167 AN: 5166

South Asian (SAS) AF: 0.576 AC: 2773 AN: 4818

European-Finnish (FIN) AF: 0.500 AC: 5277 AN: 10546

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40370 AN: 67950

Other (OTH) AF: 0.499 AC: 1048 AN: 2102

Alfa AF: 0.562 Hom.: 40924

Bravo AF: 0.496

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.53
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: rs10173528; hg19: chr2-28288392;