ENST00000419536.1:n.246+17205G>A

Variant names:

• chr1-113875221-G-A
• rs6665194
• ENST00000419536.1:n.246+17205G>A

Variant summary

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

The ENST00000419536.1(AP4B1-AS1):​n.246+17205G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,942 control chromosomes in the GnomAD database, including 14,386 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 0.42 (14386 hom., cov: 31)
• Consequence: AP4B1-AS1 ENST00000419536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 24 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AP4B1-AS1	NR_037864.1	n.246+17205G>A		intron_variant	Intron 3 of 4
AP4B1-AS1	NR_125965.1	n.415-22647G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AP4B1-AS1	ENST00000419536.1	n.246+17205G>A		intron_variant	Intron 3 of 4	2
AP4B1-AS1	ENST00000717022.1	n.441-19939G>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64081 AN: 151824 Hom.: 14381 Cov.: 31

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.422 AC: 64118 AN: 151942 Hom.: 14386 Cov.: 31 AF XY: 0.428 AC XY: 31819 AN XY: 74272

African (AFR) AF: 0.328 AC: 13573 AN: 41422

American (AMR) AF: 0.536 AC: 8180 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3472

East Asian (EAS) AF: 0.830 AC: 4299 AN: 5180

South Asian (SAS) AF: 0.341 AC: 1641 AN: 4808

European-Finnish (FIN) AF: 0.510 AC: 5384 AN: 10550

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.416 AC: 28274 AN: 67932

Other (OTH) AF: 0.447 AC: 943 AN: 2110

Alfa AF: 0.418 Hom.: 22933

Bravo AF: 0.429

Asia WGS AF: 0.554 AC: 1927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.51
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs6665194; hg19: chr1-114417843; COSMIC: COSV63084581;