1-113878691-C-T

Variant names:

• chr1-113878691-C-T
• rs11102691
• NM_001010922.3:c.*2432G>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001010922.3(BCL2L15):​c.*2432G>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 0.216 in 152,228 control chromosomes in the GnomAD database, including 4,529 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 0.22 (4523 hom., cov: 32)
  • Exomes 𝑓: 0.31 (6 hom.)
• Consequence: BCL2L15 NM_001010922.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCL2L15	NM_001010922.3	c.*2432G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000393316.8	NP_001010922.1
AP4B1-AS1	NR_037864.1	n.247-19177C>T		intron_variant	Intron 3 of 4
AP4B1-AS1	NR_125965.1	n.415-19177C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L15	ENST00000393316	c.*2432G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_001010922.3	ENSP00000376992.3
BCL2L15	ENST00000369580.3	n.3518G>A		non_coding_transcript_exon_variant	Exon 2 of 2	1
AP4B1-AS1	ENST00000419536.1	n.247-19177C>T		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32916 AN: 151976 Hom.: 4529 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.241

GnomAD4 exome AF: 0.306 AC: 41 AN: 134 Hom.: 6 Cov.: 0 AF XY: 0.278 AC XY: 20 AN XY: 72

Gnomad4 EAS exome AF: 0.306

GnomAD4 genome AF: 0.216 AC: 32907 AN: 152094 Hom.: 4523 Cov.: 32 AF XY: 0.224 AC XY: 16656 AN XY: 74334

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.240

Alfa AF: 0.230 Hom.: 4853

Bravo AF: 0.222

Asia WGS AF: 0.345 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	7.1
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11102691; hg19: chr1-114421313;