rs1746860

Positions:

• chr1-113886718-T-C

Variant summary

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

The NM_001010922.3(BCL2L15):​c.128-60A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 1,513,538 control chromosomes in the GnomAD database, including 87,904 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 0.41 (15472 hom., cov: 30)
  • Exomes 𝑓: 0.32 (72432 hom.)
• Consequence: BCL2L15 NM_001010922.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

BCL2L15 (HGNC:33624): (BCL2 like 15) Predicted to be involved in apoptotic process and regulation of apoptotic process. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

BCL2L15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL2L15	NM_001010922.3	c.128-60A>G		intron_variant		ENST00000393316.8	NP_001010922.1
AP4B1-AS1	NR_037864.1	n.247-11150T>C		intron_variant
AP4B1-AS1	NR_125965.1	n.415-11150T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL2L15	ENST00000393316.8	c.128-60A>G		intron_variant		1	NM_001010922.3	ENSP00000376992.3

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61818 AN: 151820 Hom.: 15443 Cov.: 30

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.375

GnomAD4 exome AF: 0.317 AC: 431177 AN: 1361600 Hom.: 72432 AF XY: 0.316 AC XY: 212233 AN XY: 671784

Gnomad4 AFR exome AF: 0.726

Gnomad4 AMR exome AF: 0.195

Gnomad4 ASJ exome AF: 0.408

Gnomad4 EAS exome AF: 0.0954

Gnomad4 SAS exome AF: 0.322

Gnomad4 FIN exome AF: 0.273

Gnomad4 NFE exome AF: 0.315

Gnomad4 OTH exome AF: 0.329

GnomAD4 genome AF: 0.407 AC: 61897 AN: 151938 Hom.: 15472 Cov.: 30 AF XY: 0.399 AC XY: 29655 AN XY: 74286

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.0762

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.372

Alfa AF: 0.338 Hom.: 7734

Bravo AF: 0.414

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.8
DANN	Benign	0.85

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: rs1746860; hg19: chr1-114429340; COSMIC: COSV63643009;