rs10180107

Variant names:

• chr2-28017658-T-C
• rs10180107
• NM_199191.3:c.301-7568T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199191.3(BABAM2):​c.301-7568T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,096 control chromosomes in the GnomAD database, including 41,873 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 0.73 (41873 hom., cov: 32)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BABAM2	NM_199191.3	c.301-7568T>C		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.301-7568T>C		intron_variant	Intron 4 of 11	1	NM_199191.3	ENSP00000368945.1

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111320 AN: 151980 Hom.: 41864 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.732 AC: 111364 AN: 152096 Hom.: 41873 Cov.: 32 AF XY: 0.725 AC XY: 53890 AN XY: 74338

African (AFR) AF: 0.636 AC: 26372 AN: 41468

American (AMR) AF: 0.631 AC: 9632 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2966 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1970 AN: 5170

South Asian (SAS) AF: 0.819 AC: 3952 AN: 4826

European-Finnish (FIN) AF: 0.742 AC: 7851 AN: 10578

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56111 AN: 68000

Other (OTH) AF: 0.758 AC: 1597 AN: 2106

Alfa AF: 0.713 Hom.: 17490

Bravo AF: 0.710

Asia WGS AF: 0.589 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.26
DANN	Benign	0.23
PhyloP100		-3.1
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: rs10180107; hg19: chr2-28240525;