chr12-12115592-C-T

Variant names:

• chr12-12115592-C-T
• rs7316466
• ENST00000298566.2:n.711+265C>T

Variant summary

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

The ENST00000298566.2(BCL2L14):​n.711+265C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,976 control chromosomes in the GnomAD database, including 30,961 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 0.64 (30961 hom., cov: 31)
• Consequence: BCL2L14 ENST00000298566.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

BCL2L14 (HGNC:16657): (BCL2 like 14) The protein encoded by this gene belongs to the BCL2 protein family. BCL2 family members form hetero- or homodimers and act as anti- or pro-apoptotic regulators that are involved in a wide variety of cellular activities. Overexpression of this gene has been shown to induce apoptosis in cells. Three alternatively spliced transcript variants encoding two distinct isoforms have been reported for this gene. [provided by RefSeq, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L14	ENST00000298566.2	n.711+265C>T		intron_variant	Intron 4 of 6	2		ENSP00000298566.1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96612 AN: 151858 Hom.: 30952 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.636 AC: 96669 AN: 151976 Hom.: 30961 Cov.: 31 AF XY: 0.645 AC XY: 47915 AN XY: 74262

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.661

Alfa AF: 0.633 Hom.: 13460

Bravo AF: 0.633

Asia WGS AF: 0.738 AC: 2566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7316466; hg19: chr12-12268526;