1-113884202-T-G

Position:

• chr1-113884202-T-G

Variant summary

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

The NM_001010922.3(BCL2L15):​c.250-2205A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,046 control chromosomes in the GnomAD database, including 9,509 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 0.32 (9509 hom., cov: 32)
• Consequence: BCL2L15 NM_001010922.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCL2L15	NM_001010922.3	c.250-2205A>C		intron_variant		ENST00000393316.8	NP_001010922.1
AP4B1-AS1	NR_037864.1	n.247-13666T>G		intron_variant
AP4B1-AS1	NR_125965.1	n.415-13666T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCL2L15	ENST00000393316.8	c.250-2205A>C		intron_variant		1	NM_001010922.3	ENSP00000376992.3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48893 AN: 151928 Hom.: 9514 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.342

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.322 AC: 48900 AN: 152046 Hom.: 9509 Cov.: 32 AF XY: 0.329 AC XY: 24482 AN XY: 74308

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.346

Alfa AF: 0.346 Hom.: 3792

Bravo AF: 0.324

Asia WGS AF: 0.490 AC: 1701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.72

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: rs7524200; hg19: chr1-114426824; COSMIC: COSV63642897;