1-113886839-G-A

Position:

• chr1-113886839-G-A

Variant summary

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

The NM_001010922.3(BCL2L15):​c.128-181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,944 control chromosomes in the GnomAD database, including 3,150 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 0.17 (3150 hom., cov: 32)
• Consequence: BCL2L15 NM_001010922.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952

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]

AP4B1-AS1 (HGNC:44114): (AP4B1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCL2L15	NM_001010922.3	c.128-181C>T		intron_variant		ENST00000393316.8
AP4B1-AS1	NR_125965.1	n.415-11029G>A		intron_variant, non_coding_transcript_variant
AP4B1-AS1	NR_037864.1	n.247-11029G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL2L15	ENST00000393316.8	c.128-181C>T		intron_variant		1	NM_001010922.3	P1
AP4B1-AS1	ENST00000419536.1	n.247-11029G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25134 AN: 151828 Hom.: 3158 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.165 AC: 25122 AN: 151944 Hom.: 3150 Cov.: 32 AF XY: 0.170 AC XY: 12626 AN XY: 74214

Gnomad4 AFR AF: 0.0397

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.187

Alfa AF: 0.175 Hom.: 5355

Bravo AF: 0.177

Asia WGS AF: 0.320 AC: 1110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.66

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: rs2358994; hg19: chr1-114429461;