rs6547829

chr2-28101002-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.571-28269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.075 in 152,210 control chromosomes in the GnomAD database, including 505 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 0.075 (505 hom., cov: 32)
• Consequence: BABAM2 NM_199191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

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=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BABAM2	NM_199191.3	c.571-28269C>T		intron_variant		ENST00000379624.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BABAM2	ENST00000379624.6	c.571-28269C>T		intron_variant		1	NM_199191.3	P1

Frequencies

GnomAD3 genomes AF: 0.0752 AC: 11433 AN: 152092 Hom.: 507 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.0825

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0750 AC: 11423 AN: 152210 Hom.: 505 Cov.: 32 AF XY: 0.0766 AC XY: 5703 AN XY: 74410

Gnomad4 AFR AF: 0.0288

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0823

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.0915

Gnomad4 OTH AF: 0.0914

Alfa AF: 0.0904 Hom.: 994

Bravo AF: 0.0708

Asia WGS AF: 0.0990 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	9.3
Dann	Benign	0.75

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: rs6547829; hg19: chr2-28323869;