rs2448050

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-12096290-G-A
• chr12-12096290-G-C
• chr12-12096290-G-T

Variant summary

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

The NM_138723.2(BCL2L14):​c.945+1360G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 522,798 control chromosomes in the GnomAD database, including 81,399 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 0.51 (20311 hom., cov: 31)
  • Exomes 𝑓: 0.57 (61088 hom.)
• Consequence: BCL2L14 NM_138723.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 7 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138723.2. 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
	BCL2L14	NM_138723.2	MANE Select	c.945+1360G>A		intron	N/A	NP_620049.1
	BCL2L14	NM_001370268.1		c.945+1360G>A		intron	N/A	NP_001357197.1
	BCL2L14	NM_001370269.1		c.945+1360G>A		intron	N/A	NP_001357198.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L14	ENST00000308721.9	TSL:1 MANE Select	c.945+1360G>A		intron	N/A	ENSP00000309132.4
	BCL2L14	ENST00000396367.5	TSL:1	c.945+1360G>A		intron	N/A	ENSP00000379653.1
	BCL2L14	ENST00000266434.8	TSL:1	c.*339+1360G>A		intron	N/A	ENSP00000266434.4

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77307 AN: 151654 Hom.: 20309 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.497

GnomAD4 exome AF: 0.573 AC: 212714 AN: 371026 Hom.: 61088 AF XY: 0.573 AC XY: 100505 AN XY: 175278

African (AFR) AF: 0.352 AC: 2344 AN: 6664

American (AMR) AF: 0.495 AC: 210 AN: 424

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1234 AN: 2374

East Asian (EAS) AF: 0.643 AC: 987 AN: 1536

South Asian (SAS) AF: 0.577 AC: 4157 AN: 7210

European-Finnish (FIN) AF: 0.524 AC: 65 AN: 124

Middle Eastern (MID) AF: 0.435 AC: 317 AN: 728

European-Non Finnish (NFE) AF: 0.578 AC: 196583 AN: 339954

Other (OTH) AF: 0.568 AC: 6817 AN: 12012

GnomAD4 genome AF: 0.510 AC: 77336 AN: 151772 Hom.: 20311 Cov.: 31 AF XY: 0.509 AC XY: 37744 AN XY: 74176

African (AFR) AF: 0.380 AC: 15726 AN: 41342

American (AMR) AF: 0.488 AC: 7447 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1752 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3371 AN: 5166

South Asian (SAS) AF: 0.592 AC: 2835 AN: 4792

European-Finnish (FIN) AF: 0.546 AC: 5729 AN: 10500

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38806 AN: 67940

Other (OTH) AF: 0.495 AC: 1044 AN: 2110

Alfa AF: 0.549 Hom.: 99270

Bravo AF: 0.499

Asia WGS AF: 0.555 AC: 1930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.74
PhyloP100		-0.65
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: rs2448050; hg19: chr12-12249224;