1-113874815-C-G

Variant names:

• chr1-113874815-C-G
• rs1235005
• ENST00000419536.1:n.246+16799C>G

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+16799C>G variant causes a intron 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 ENST00000419536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254
• Publications: 19 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=-0.83).
• 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 rank	MANE	Protein	UniProt
AP4B1-AS1	NR_037864.1	n.246+16799C>G		intron_variant	Intron 3 of 4
AP4B1-AS1	NR_125965.1	n.415-23053C>G		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+16799C>G		intron_variant	Intron 3 of 4	2
AP4B1-AS1	ENST00000717022.1	n.441-20345C>G		intron_variant	Intron 3 of 5

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

African (AFR) AF: 0.685 AC: 28355 AN: 41416

American (AMR) AF: 0.468 AC: 7142 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3470

East Asian (EAS) AF: 0.169 AC: 873 AN: 5170

South Asian (SAS) AF: 0.653 AC: 3145 AN: 4814

European-Finnish (FIN) AF: 0.490 AC: 5183 AN: 10570

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.584 AC: 39659 AN: 67952

Other (OTH) AF: 0.557 AC: 1176 AN: 2112

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
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1235005; hg19: chr1-114417437;