rs13402525

Variant names:

• chr2-28091991-G-T
• rs13402525
• NM_199191.3:c.571-37280G>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.571-37280G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,672 control chromosomes in the GnomAD database, including 22,007 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 0.52 (22007 hom., cov: 31)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 6 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 = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BABAM2	NM_199191.3	c.571-37280G>T		intron_variant	Intron 6 of 11	ENST00000379624.6	NP_954661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BABAM2	ENST00000379624.6	c.571-37280G>T		intron_variant	Intron 6 of 11	1	NM_199191.3	ENSP00000368945.1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78664 AN: 151554 Hom.: 22012 Cov.: 31

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.519 AC: 78667 AN: 151672 Hom.: 22007 Cov.: 31 AF XY: 0.509 AC XY: 37743 AN XY: 74084

African (AFR) AF: 0.330 AC: 13629 AN: 41328

American (AMR) AF: 0.456 AC: 6945 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2172 AN: 3460

East Asian (EAS) AF: 0.277 AC: 1426 AN: 5148

South Asian (SAS) AF: 0.592 AC: 2848 AN: 4808

European-Finnish (FIN) AF: 0.537 AC: 5640 AN: 10506

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44089 AN: 67880

Other (OTH) AF: 0.541 AC: 1141 AN: 2110

Alfa AF: 0.614 Hom.: 14942

Bravo AF: 0.500

Asia WGS AF: 0.427 AC: 1483 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.33
PhyloP100		1.1
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: rs13402525; hg19: chr2-28314858;