rs13402525

Positions:

• chr2-28091991-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• 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/exons	MANE	UniProt
BABAM2	NM_199191.3	c.571-37280G>T		intron_variant		ENST00000379624.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BABAM2	ENST00000379624.6	c.571-37280G>T		intron_variant		1	NM_199191.3	P1

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

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.541

Alfa AF: 0.613 Hom.: 13429

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

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: rs13402525; hg19: chr2-28314858;