chr1-113877138-G-C

Variant names:

• chr1-113877138-G-C
• rs1217384
• NM_001010922.3:c.*3985C>G

Variant summary

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

The NM_001010922.3(BCL2L15):​c.*3985C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 151,938 control chromosomes in the GnomAD database, including 46,824 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 0.78 (46824 hom., cov: 28)
• Consequence: BCL2L15 NM_001010922.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802
• Publications: 12 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L15	NM_001010922.3	MANE Select	c.*3985C>G		3_prime_UTR	Exon 4 of 4	NP_001010922.1
	AP4B1-AS1	NR_037864.1		n.246+19122G>C		intron	N/A
	AP4B1-AS1	NR_125965.1		n.415-20730G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L15	ENST00000393316.8	TSL:1 MANE Select	c.*3985C>G		3_prime_UTR	Exon 4 of 4	ENSP00000376992.3
	AP4B1-AS1	ENST00000419536.1	TSL:2	n.246+19122G>C		intron	N/A
	AP4B1-AS1	ENST00000717022.1		n.441-18022G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117917 AN: 151820 Hom.: 46768 Cov.: 28

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.777 AC: 118033 AN: 151938 Hom.: 46824 Cov.: 28 AF XY: 0.777 AC XY: 57671 AN XY: 74228

African (AFR) AF: 0.939 AC: 38946 AN: 41466

American (AMR) AF: 0.764 AC: 11655 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2407 AN: 3460

East Asian (EAS) AF: 0.908 AC: 4690 AN: 5164

South Asian (SAS) AF: 0.608 AC: 2921 AN: 4802

European-Finnish (FIN) AF: 0.749 AC: 7889 AN: 10532

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.693 AC: 47108 AN: 67952

Other (OTH) AF: 0.751 AC: 1580 AN: 2104

Alfa AF: 0.746 Hom.: 5008

Bravo AF: 0.787

Asia WGS AF: 0.763 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.71
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs1217384; hg19: chr1-114419760;