rs1539438

Variant names:

• chr1-113887734-C-G
• rs1539438
• ENST00000419536.1:n.247-10134C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-113887734-C-G
• chr1-113887734-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000419536.1(AP4B1-AS1):​n.247-10134C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: AP4B1-AS1 ENST00000419536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 21 publications found

Genes affected

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

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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419536.1. 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
	AP4B1-AS1	NR_037864.1		n.247-10134C>G		intron	N/A
	AP4B1-AS1	NR_125965.1		n.415-10134C>G		intron	N/A
	BCL2L15	NM_001010922.3	MANE Select	c.-359G>C		upstream_gene	N/A	NP_001010922.1	Q53EI7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AP4B1-AS1	ENST00000419536.1	TSL:2	n.247-10134C>G		intron	N/A
	AP4B1-AS1	ENST00000717022.1		n.441-7426C>G		intron	N/A
	BCL2L15	ENST00000393316.8	TSL:1 MANE Select	c.-359G>C		upstream_gene	N/A	ENSP00000376992.3	Q5TBC7-1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.62
DANN	Benign	0.44
PhyloP100		-0.66
PromoterAI		0.088	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1539438; hg19: chr1-114430356;