2-32518017-C-T

Variant names:

• chr2-32518017-C-T
• rs2069213
• NM_016252.4:c.11350-237C>T

Variant summary

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

The NM_016252.4(BIRC6):​c.11350-237C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,526 control chromosomes in the GnomAD database, including 34,673 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 0.67 (34673 hom., cov: 29)
• Consequence: BIRC6 NM_016252.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 3 publications found

Genes affected

BIRC6 (HGNC:13516): (baculoviral IAP repeat containing 6) This gene encodes a protein with a BIR (baculoviral inhibition of apoptosis protein repeat) domain and a UBCc (ubiquitin-conjugating enzyme E2, catalytic) domain. This protein inhibits apoptosis by facilitating the degradation of apoptotic proteins by ubiquitination. [provided by RefSeq, Jul 2008]

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 = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016252.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIRC6	NM_016252.4	MANE Select	c.11350-237C>T		intron	N/A	NP_057336.3	Q9NR09
	BIRC6	NM_001378125.1		c.11347-237C>T		intron	N/A	NP_001365054.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIRC6	ENST00000421745.7	TSL:1 MANE Select	c.11350-237C>T		intron	N/A	ENSP00000393596.2	Q9NR09
	BIRC6	ENST00000700518.1		c.11299-237C>T		intron	N/A	ENSP00000515025.1	A0A8V8TQB4
	BIRC6	ENST00000700519.1		c.11290-237C>T		intron	N/A	ENSP00000515026.1	A0A8V8TR92

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101205 AN: 151412 Hom.: 34625 Cov.: 29

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.669 AC: 101306 AN: 151526 Hom.: 34673 Cov.: 29 AF XY: 0.665 AC XY: 49252 AN XY: 74028

African (AFR) AF: 0.786 AC: 32524 AN: 41362

American (AMR) AF: 0.660 AC: 10040 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2302 AN: 3466

East Asian (EAS) AF: 0.310 AC: 1602 AN: 5160

South Asian (SAS) AF: 0.472 AC: 2262 AN: 4790

European-Finnish (FIN) AF: 0.670 AC: 6934 AN: 10346

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43433 AN: 67884

Other (OTH) AF: 0.652 AC: 1374 AN: 2106

Alfa AF: 0.627 Hom.: 7769

Bravo AF: 0.676

Asia WGS AF: 0.414 AC: 1444 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.41
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2069213; hg19: chr2-32743084;