chr12-12096290-G-T

Variant names:

• chr12-12096290-G-T
• rs2448050
• NM_138723.2:c.945+1360G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138723.2(BCL2L14):​c.945+1360G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BCL2L14 NM_138723.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL2L14	NM_138723.2	c.945+1360G>T		intron_variant	Intron 5 of 5	ENST00000308721.9	NP_620049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L14	ENST00000308721.9	c.945+1360G>T		intron_variant	Intron 5 of 5	1	NM_138723.2	ENSP00000309132.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 372974 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 176186

African (AFR) AF: 0.00 AC: 0 AN: 6692

American (AMR) AF: 0.00 AC: 0 AN: 428

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2384

East Asian (EAS) AF: 0.00 AC: 0 AN: 1544

South Asian (SAS) AF: 0.00 AC: 0 AN: 7238

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 124

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 728

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 341746

Other (OTH) AF: 0.00 AC: 0 AN: 12090

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.37
DANN	Benign	0.73
PhyloP100		-0.65

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: rs2448050; hg19: chr12-12249224;