rs10175508

Variant names:

• chr2-27990557-C-T
• rs10175508
• NM_199191.3:c.300+2470C>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.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
• 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=-0.9).
• 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 rank	MANE	Protein	UniProt
BABAM2	NM_199191.3	c.300+2470C>T		intron_variant	Intron 4 of 11	ENST00000379624.6	NP_954661.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BABAM2	ENST00000379624.6	c.300+2470C>T		intron_variant	Intron 4 of 11	1	NM_199191.3	ENSP00000368945.1

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

African (AFR) AF: 0.478 AC: 19746 AN: 41346

American (AMR) AF: 0.588 AC: 8972 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2597 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1968 AN: 5164

South Asian (SAS) AF: 0.712 AC: 3423 AN: 4808

European-Finnish (FIN) AF: 0.678 AC: 7143 AN: 10538

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53153 AN: 67970

Other (OTH) AF: 0.690 AC: 1457 AN: 2112

Alfa AF: 0.743 Hom.: 21717

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
PhyloP100		-1.8
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: rs10175508; hg19: chr2-28213424;