rs885720

Variant names:

• chr12-12095165-A-G
• rs885720
• NM_138723.2:c.945+235A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-12095165-A-G
• chr12-12095165-A-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+235A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 984,812 control chromosomes in the GnomAD database, including 310,523 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 0.71 (39801 hom., cov: 30)
  • Exomes 𝑓: 0.80 (270722 hom.)
• Consequence: BCL2L14 NM_138723.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 8 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL2L14	NM_138723.2	c.945+235A>G		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+235A>G		intron_variant	Intron 5 of 5	1	NM_138723.2	ENSP00000309132.4

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108147 AN: 151770 Hom.: 39775 Cov.: 30

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.743

GnomAD4 exome AF: 0.805 AC: 670268 AN: 832926 Hom.: 270722 Cov.: 35 AF XY: 0.805 AC XY: 309595 AN XY: 384634

African (AFR) AF: 0.498 AC: 7857 AN: 15776

American (AMR) AF: 0.660 AC: 649 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 4221 AN: 5152

East Asian (EAS) AF: 0.649 AC: 2351 AN: 3624

South Asian (SAS) AF: 0.742 AC: 12206 AN: 16458

European-Finnish (FIN) AF: 0.808 AC: 223 AN: 276

Middle Eastern (MID) AF: 0.797 AC: 1291 AN: 1620

European-Non Finnish (NFE) AF: 0.814 AC: 619918 AN: 761748

Other (OTH) AF: 0.790 AC: 21552 AN: 27288

GnomAD4 genome AF: 0.712 AC: 108217 AN: 151886 Hom.: 39801 Cov.: 30 AF XY: 0.713 AC XY: 52935 AN XY: 74230

African (AFR) AF: 0.520 AC: 21488 AN: 41350

American (AMR) AF: 0.683 AC: 10421 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2874 AN: 3464

East Asian (EAS) AF: 0.676 AC: 3493 AN: 5164

South Asian (SAS) AF: 0.740 AC: 3549 AN: 4798

European-Finnish (FIN) AF: 0.809 AC: 8550 AN: 10568

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55281 AN: 67964

Other (OTH) AF: 0.739 AC: 1557 AN: 2106

Alfa AF: 0.782 Hom.: 78630

Bravo AF: 0.694

Asia WGS AF: 0.669 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.21
DANN	Benign	0.77
PhyloP100		-2.9
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: rs885720; hg19: chr12-12248099;