rs7601155

chr2-28124815-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.571-4456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 152,068 control chromosomes in the GnomAD database, including 481 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 0.068 (481 hom., cov: 32)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BABAM2	NM_199191.3	c.571-4456C>T		intron_variant		ENST00000379624.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BABAM2	ENST00000379624.6	c.571-4456C>T		intron_variant		1	NM_199191.3	P1

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10317 AN: 151950 Hom.: 482 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0472

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.0258

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0679 AC: 10322 AN: 152068 Hom.: 481 Cov.: 32 AF XY: 0.0681 AC XY: 5058 AN XY: 74314

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0560

Gnomad4 ASJ AF: 0.0472

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.0490

Gnomad4 FIN AF: 0.0258

Gnomad4 NFE AF: 0.0389

Gnomad4 OTH AF: 0.0762

Alfa AF: 0.0507 Hom.: 126

Bravo AF: 0.0712

Asia WGS AF: 0.0970 AC: 335 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	0.94
Dann	Benign	0.68

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: rs7601155; hg19: chr2-28347682;