ENST00000369580.3:n.3518G>T

Variant names:

• chr1-113878691-C-A
• rs11102691
• ENST00000369580.3:n.3518G>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000369580.3(BCL2L15):​n.3518G>T variant causes a non coding transcript exon 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: BCL2L15 ENST00000369580.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.41
• Publications: 16 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL2L15	ENST00000369580.3	n.3518G>T		non_coding_transcript_exon_variant	Exon 2 of 2	1
BCL2L15	ENST00000393316.8	c.*2432G>T		3_prime_UTR_variant	Exon 4 of 4	1	NM_001010922.3	ENSP00000376992.3
AP4B1-AS1	ENST00000419536.1	n.247-19177C>A		intron_variant	Intron 3 of 4	2
AP4B1-AS1	ENST00000717022.1	n.441-16469C>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	6.5
DANN	Benign	0.76
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs11102691; hg19: chr1-114421313;