11-102347075-A-G

Variant names:

• chr11-102347075-A-G
• rs1317775
• ENST00000687499.3:n.535T>C

Variant summary

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

The ENST00000687499.3(ENSG00000288833):​n.535T>C 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 0.508 in 24,030 control chromosomes in the GnomAD database, including 655 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 0.51 (655 hom., cov: 25)
  • Exomes 𝑓: 0.083 (0 hom.)
• Consequence: ENSG00000288833 ENST00000687499.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.941
• Publications: 2 publications found

Genes affected

ENSG00000288833 (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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687499.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIRC2	NM_001166.5	MANE Select	c.-1559A>G		upstream_gene	N/A	NP_001157.1
	BIRC2	NM_001256166.2		c.-303A>G		upstream_gene	N/A	NP_001243095.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288833	ENST00000687499.3		n.535T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288833	ENST00000764978.1		n.125T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000288833	ENST00000764979.1		n.71T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.508 AC: 12177 AN: 23962 Hom.: 647 Cov.: 25

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.511

GnomAD4 exome AF: 0.0833 AC: 2 AN: 24 Hom.: 0 AF XY: 0.0625 AC XY: 1 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0833 AC: 2 AN: 24

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.509 AC: 12209 AN: 24006 Hom.: 655 Cov.: 25 AF XY: 0.507 AC XY: 5620 AN XY: 11076

African (AFR) AF: 0.531 AC: 5864 AN: 11050

American (AMR) AF: 0.494 AC: 798 AN: 1616

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 247 AN: 512

East Asian (EAS) AF: 0.362 AC: 29 AN: 80

South Asian (SAS) AF: 0.413 AC: 85 AN: 206

European-Finnish (FIN) AF: 0.451 AC: 242 AN: 536

Middle Eastern (MID) AF: 0.500 AC: 12 AN: 24

European-Non Finnish (NFE) AF: 0.493 AC: 4712 AN: 9556

Other (OTH) AF: 0.515 AC: 136 AN: 264

Alfa AF: 0.0369 Hom.: 24

Bravo AF: 0.0839

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.36
PhyloP100		-0.94
PromoterAI		0.073	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1317775; hg19: chr11-102217806;