rs17820747

Variant names:

• chr2-32476619-A-C
• rs17820747
• NM_016252.4:c.6852+275A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-32476619-A-C
• chr2-32476619-A-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.6852+275A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,098 control chromosomes in the GnomAD database, including 3,421 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 0.21 (3421 hom., cov: 32)
• Consequence: BIRC6 NM_016252.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.279 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIRC6	NM_016252.4	MANE Select	c.6852+275A>C		intron	N/A	NP_057336.3
	BIRC6	NM_001378125.1		c.6849+275A>C		intron	N/A	NP_001365054.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BIRC6	ENST00000421745.7	TSL:1 MANE Select	c.6852+275A>C		intron	N/A	ENSP00000393596.2
	BIRC6	ENST00000700518.1		c.6801+275A>C		intron	N/A	ENSP00000515025.1
	BIRC6	ENST00000700519.1		c.6792+275A>C		intron	N/A	ENSP00000515026.1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31301 AN: 151980 Hom.: 3418 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0425

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.206 AC: 31318 AN: 152098 Hom.: 3421 Cov.: 32 AF XY: 0.207 AC XY: 15377 AN XY: 74338

African (AFR) AF: 0.145 AC: 6031 AN: 41530

American (AMR) AF: 0.286 AC: 4366 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.0418 AC: 217 AN: 5190

South Asian (SAS) AF: 0.176 AC: 852 AN: 4828

European-Finnish (FIN) AF: 0.232 AC: 2450 AN: 10560

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15623 AN: 67932

Other (OTH) AF: 0.211 AC: 445 AN: 2112

Alfa AF: 0.210 Hom.: 2750

Bravo AF: 0.210

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.95
DANN	Benign	0.77
PhyloP100		-0.73
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: rs17820747; hg19: chr2-32701687;