1-113881031-C-T

Position:

• chr1-113881031-C-T

Variant summary

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

The NM_001010922.3(BCL2L15):​c.*92G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,581,740 control chromosomes in the GnomAD database, including 91,087 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 0.43 (18045 hom., cov: 32)
  • Exomes 𝑓: 0.31 (73042 hom.)
• Consequence: BCL2L15 NM_001010922.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL2L15	NM_001010922.3	c.*92G>A		3_prime_UTR_variant	4/4	ENST00000393316.8	NP_001010922.1
AP4B1-AS1	NR_037864.1	n.247-16837C>T		intron_variant
AP4B1-AS1	NR_125965.1	n.415-16837C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL2L15	ENST00000393316	c.*92G>A		3_prime_UTR_variant	4/4	1	NM_001010922.3	ENSP00000376992.3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64719 AN: 151932 Hom.: 17994 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.386

GnomAD4 exome AF: 0.305 AC: 436714 AN: 1429690 Hom.: 73042 Cov.: 25 AF XY: 0.304 AC XY: 216624 AN XY: 712652

Gnomad4 AFR exome AF: 0.819

Gnomad4 AMR exome AF: 0.179

Gnomad4 ASJ exome AF: 0.396

Gnomad4 EAS exome AF: 0.0949

Gnomad4 SAS exome AF: 0.297

Gnomad4 FIN exome AF: 0.272

Gnomad4 NFE exome AF: 0.302

Gnomad4 OTH exome AF: 0.327

GnomAD4 genome AF: 0.426 AC: 64824 AN: 152050 Hom.: 18045 Cov.: 32 AF XY: 0.417 AC XY: 31015 AN XY: 74326

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.0774

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.383

Alfa AF: 0.302 Hom.: 12729

Bravo AF: 0.437

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.096
DANN	Benign	0.41

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: rs1217382; hg19: chr1-114423653; COSMIC: COSV63642946; COSMIC: COSV63642946;