1-113884202-T-G

Variant names:

• chr1-113884202-T-G
• rs7524200
• NM_001010922.3:c.250-2205A>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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.250-2205A>C		intron	N/A	NP_001010922.1
	AP4B1-AS1	NR_037864.1		n.247-13666T>G		intron	N/A
	AP4B1-AS1	NR_125965.1		n.415-13666T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L15	ENST00000393316.8	TSL:1 MANE Select	c.250-2205A>C		intron	N/A	ENSP00000376992.3
	BCL2L15	ENST00000471267.1	TSL:1	c.249+2335A>C		intron	N/A	ENSP00000417458.1
	BCL2L15	ENST00000393320.3	TSL:1	c.127+3047A>C		intron	N/A	ENSP00000376995.3

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

African (AFR) AF: 0.130 AC: 5378 AN: 41522

American (AMR) AF: 0.459 AC: 7006 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4012 AN: 5160

South Asian (SAS) AF: 0.270 AC: 1301 AN: 4826

European-Finnish (FIN) AF: 0.443 AC: 4666 AN: 10542

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24451 AN: 67948

Other (OTH) AF: 0.346 AC: 728 AN: 2104

Alfa AF: 0.348 Hom.: 6399

Bravo AF: 0.324

Asia WGS AF: 0.490 AC: 1701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.72
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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