1-113874815-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125965.1(AP4B1-AS1):n.415-23053C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,978 control chromosomes in the GnomAD database, including 26,628 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 0.58 (26628 hom., cov: 31)
• Consequence: AP4B1-AS1 NR_125965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AP4B1-AS1	NR_125965.1	n.415-23053C>G		intron_variant, non_coding_transcript_variant
AP4B1-AS1	NR_037864.1	n.246+16799C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AP4B1-AS1	ENST00000419536.1	n.246+16799C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88306 AN: 151862 Hom.: 26599 Cov.: 31

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.582 AC: 88384 AN: 151978 Hom.: 26628 Cov.: 31 AF XY: 0.574 AC XY: 42668 AN XY: 74288

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.557

Alfa AF: 0.474 Hom.: 1389

Bravo AF: 0.576

Asia WGS AF: 0.443 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.6
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1235005; hg19: chr1-114417437;