1-113891324-G-A

Variant names:

• chr1-113891324-G-A
• rs1217393
• ENST00000419536.1:n.247-6544G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000419536.1(AP4B1-AS1):​n.247-6544G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,954 control chromosomes in the GnomAD database, including 15,479 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 0.41 (15479 hom., cov: 32)
• Consequence: AP4B1-AS1 ENST00000419536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AP4B1-AS1	NR_037864.1		n.247-6544G>A		intron	N/A
	AP4B1-AS1	NR_125965.1		n.415-6544G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AP4B1-AS1	ENST00000419536.1	TSL:2	n.247-6544G>A		intron	N/A
	AP4B1-AS1	ENST00000717022.1		n.441-3836G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61850 AN: 151836 Hom.: 15450 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.408 AC: 61928 AN: 151954 Hom.: 15479 Cov.: 32 AF XY: 0.399 AC XY: 29638 AN XY: 74258

African (AFR) AF: 0.704 AC: 29175 AN: 41432

American (AMR) AF: 0.257 AC: 3926 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3466

East Asian (EAS) AF: 0.0762 AC: 395 AN: 5186

South Asian (SAS) AF: 0.301 AC: 1449 AN: 4816

European-Finnish (FIN) AF: 0.259 AC: 2724 AN: 10528

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21672 AN: 67950

Other (OTH) AF: 0.375 AC: 794 AN: 2116

Alfa AF: 0.384 Hom.: 1625

Bravo AF: 0.414

Asia WGS AF: 0.218 AC: 759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.81
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1217393; hg19: chr1-114433946;