1-113887734-C-T

Variant names:

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

Variant summary

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

The ENST00000419536.1(AP4B1-AS1):​n.247-10134C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,178 control chromosomes in the GnomAD database, including 44,823 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 0.76 (44823 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AP4B1-AS1	NR_037864.1	n.247-10134C>T		intron_variant	Intron 3 of 4
AP4B1-AS1	NR_125965.1	n.415-10134C>T		intron_variant	Intron 3 of 4
BCL2L15	NM_001010922.3	c.-359G>A		upstream_gene_variant		ENST00000393316.8	NP_001010922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AP4B1-AS1	ENST00000419536.1	n.247-10134C>T		intron_variant	Intron 3 of 4	2
AP4B1-AS1	ENST00000717022.1	n.441-7426C>T		intron_variant	Intron 3 of 5
BCL2L15	ENST00000393316.8	c.-359G>A		upstream_gene_variant		1	NM_001010922.3	ENSP00000376992.3

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115321 AN: 152060 Hom.: 44770 Cov.: 32

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.759 AC: 115431 AN: 152178 Hom.: 44823 Cov.: 32 AF XY: 0.757 AC XY: 56319 AN XY: 74400

African (AFR) AF: 0.935 AC: 38836 AN: 41546

American (AMR) AF: 0.728 AC: 11128 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2348 AN: 3470

East Asian (EAS) AF: 0.854 AC: 4424 AN: 5182

South Asian (SAS) AF: 0.570 AC: 2750 AN: 4826

European-Finnish (FIN) AF: 0.701 AC: 7408 AN: 10574

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46174 AN: 67982

Other (OTH) AF: 0.736 AC: 1553 AN: 2110

Alfa AF: 0.696 Hom.: 92729

Bravo AF: 0.770

Asia WGS AF: 0.713 AC: 2478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.74
DANN	Benign	0.54
PhyloP100		-0.66
PromoterAI		0.0096	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;