rs10175508

chr2-27990557-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199191.3(BABAM2):c.300+2470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,858 control chromosomes in the GnomAD database, including 34,147 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 0.65 (34147 hom., cov: 30)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BABAM2	NM_199191.3	c.300+2470C>T		intron_variant		ENST00000379624.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BABAM2	ENST00000379624.6	c.300+2470C>T		intron_variant		1	NM_199191.3	P1

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99292 AN: 151740 Hom.: 34153 Cov.: 30

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.654 AC: 99304 AN: 151858 Hom.: 34147 Cov.: 30 AF XY: 0.646 AC XY: 47921 AN XY: 74218

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.690

Alfa AF: 0.744 Hom.: 19418

Bravo AF: 0.633

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.013
Dann	Benign	0.21

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: rs10175508; hg19: chr2-28213424;