rs1318199

Positions:

• chr11-102347161-G-C

Variant summary

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

The ENST00000687499.2(ENSG00000288833):​n.50C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0437 in 152,308 control chromosomes in the GnomAD database, including 198 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 0.044 (198 hom., cov: 35)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENST00000687499.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310

Genes affected

(HGNC:):

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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000687499.2	n.50C>G		non_coding_transcript_exon_variant	1/1
BIRC2	ENST00000527808.1			upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0438 AC: 6660 AN: 152190 Hom.: 198 Cov.: 35

Gnomad AFR AF: 0.0143

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0425

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 22

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0437 AC: 6661 AN: 152308 Hom.: 198 Cov.: 35 AF XY: 0.0407 AC XY: 3035 AN XY: 74490

Gnomad4 AFR AF: 0.0143

Gnomad4 AMR AF: 0.0375

Gnomad4 ASJ AF: 0.0689

Gnomad4 EAS AF: 0.00560

Gnomad4 SAS AF: 0.0174

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0596 Hom.: 45

Bravo AF: 0.0429

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.3
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1318199; hg19: chr11-102217892;