1-113877706-C-T

Variant names:

• chr1-113877706-C-T
• rs12566340
• NM_001010922.3:c.*3417G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010922.3(BCL2L15):​c.*3417G>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 0.215 in 152,004 control chromosomes in the GnomAD database, including 4,640 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 0.21 (4640 hom., cov: 32)
• Consequence: BCL2L15 NM_001010922.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 23 publications found

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

Our verdict: Benign. The variant received -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 = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010922.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L15	NM_001010922.3	MANE Select	c.*3417G>A		3_prime_UTR	Exon 4 of 4	NP_001010922.1	Q53EI7
	AP4B1-AS1	NR_037864.1		n.246+19690C>T		intron	N/A
	AP4B1-AS1	NR_125965.1		n.415-20162C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L15	ENST00000393316.8	TSL:1 MANE Select	c.*3417G>A		3_prime_UTR	Exon 4 of 4	ENSP00000376992.3	Q5TBC7-1
	AP4B1-AS1	ENST00000419536.1	TSL:2	n.246+19690C>T		intron	N/A
	AP4B1-AS1	ENST00000717022.1		n.441-17454C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32621 AN: 151886 Hom.: 4644 Cov.: 32

Gnomad AFR AF: 0.0595

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.215 AC: 32616 AN: 152004 Hom.: 4640 Cov.: 32 AF XY: 0.222 AC XY: 16472 AN XY: 74274

African (AFR) AF: 0.0594 AC: 2464 AN: 41482

American (AMR) AF: 0.349 AC: 5340 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3470

East Asian (EAS) AF: 0.619 AC: 3196 AN: 5164

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4818

European-Finnish (FIN) AF: 0.309 AC: 3251 AN: 10534

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15743 AN: 67944

Other (OTH) AF: 0.245 AC: 517 AN: 2110

Alfa AF: 0.227 Hom.: 8381

Bravo AF: 0.219

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.55
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs12566340; hg19: chr1-114420328;