2-28086710-A-G

Variant names:

• chr2-28086710-A-G
• rs10173426
• NM_199191.3:c.570+40911A>G

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+40911A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,118 control chromosomes in the GnomAD database, including 22,215 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 (22215 hom., cov: 32)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537
• Publications: 4 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=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BABAM2	NM_199191.3	c.570+40911A>G		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.570+40911A>G		intron_variant	Intron 6 of 11	1	NM_199191.3	ENSP00000368945.1

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79175 AN: 152000 Hom.: 22220 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.521 AC: 79178 AN: 152118 Hom.: 22215 Cov.: 32 AF XY: 0.511 AC XY: 38018 AN XY: 74358

African (AFR) AF: 0.332 AC: 13805 AN: 41520

American (AMR) AF: 0.458 AC: 6990 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2183 AN: 3468

East Asian (EAS) AF: 0.290 AC: 1504 AN: 5180

South Asian (SAS) AF: 0.595 AC: 2871 AN: 4826

European-Finnish (FIN) AF: 0.536 AC: 5668 AN: 10572

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44224 AN: 67954

Other (OTH) AF: 0.544 AC: 1149 AN: 2114

Alfa AF: 0.603 Hom.: 12967

Bravo AF: 0.503

Asia WGS AF: 0.433 AC: 1506 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.83
PhyloP100		0.54
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: rs10173426; hg19: chr2-28309577;