rs1943781

chr11-102364410-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001166.5(BIRC2):c.1123+694G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,698 control chromosomes in the GnomAD database, including 3,344 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 0.18 (3344 hom., cov: 30)
• Consequence: BIRC2 NM_001166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

Genes affected

BIRC2 (HGNC:590): (baculoviral IAP repeat containing 2) The protein encoded by this gene is a member of a family of proteins that inhibits apoptosis by binding to tumor necrosis factor receptor-associated factors TRAF1 and TRAF2, probably by interfering with activation of ICE-like proteases. This encoded protein inhibits apoptosis induced by serum deprivation and menadione, a potent inducer of free radicals. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BIRC2	NM_001166.5	c.1123+694G>A		intron_variant		ENST00000227758.7
BIRC2	NM_001256163.1	c.1123+694G>A		intron_variant
BIRC2	NM_001256166.2	c.976+694G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BIRC2	ENST00000227758.7	c.1123+694G>A		intron_variant		1	NM_001166.5

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26889 AN: 151580 Hom.: 3333 Cov.: 30

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.0980

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00505

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.0591

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.178 AC: 26932 AN: 151698 Hom.: 3344 Cov.: 30 AF XY: 0.170 AC XY: 12598 AN XY: 74156

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.00526

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.0591

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.158

Alfa AF: 0.141 Hom.: 1697

Bravo AF: 0.189

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.3
Dann	Benign	0.64

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: rs1943781; hg19: chr11-102235141;