2-32518017-C-T

Position:

• chr2-32518017-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BIRC6	NM_016252.4	c.11350-237C>T		intron_variant		ENST00000421745.7	NP_057336.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BIRC6	ENST00000421745.7	c.11350-237C>T		intron_variant		1	NM_016252.4	ENSP00000393596.2

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

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.652

Alfa AF: 0.624 Hom.: 7547

Bravo AF: 0.676

Asia WGS AF: 0.414 AC: 1444 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.41

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: rs2069213; hg19: chr2-32743084;