rs1217411

Variant names:

• chr1-113813503-A-G
• rs1217411
• ENST00000702317.2:n.911A>G

Variant summary

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

The ENST00000702317.2(AP4B1-AS1):​n.911A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,754 control chromosomes in the GnomAD database, including 24,568 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 0.56 (24568 hom., cov: 30)
• Consequence: AP4B1-AS1 ENST00000702317.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AP4B1-AS1	NR_125965.1	n.214+678A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AP4B1-AS1	ENST00000702317.2	n.911A>G		non_coding_transcript_exon_variant	Exon 1 of 1
AP4B1-AS1	ENST00000418238.3	n.247+678A>G		intron_variant	Intron 1 of 1	3
AP4B1-AS1	ENST00000429398.5	n.235-884A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84987 AN: 151636 Hom.: 24542 Cov.: 30

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.561 AC: 85062 AN: 151754 Hom.: 24568 Cov.: 30 AF XY: 0.555 AC XY: 41177 AN XY: 74148

African (AFR) AF: 0.635 AC: 26257 AN: 41322

American (AMR) AF: 0.451 AC: 6869 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3472

East Asian (EAS) AF: 0.161 AC: 832 AN: 5170

South Asian (SAS) AF: 0.651 AC: 3134 AN: 4814

European-Finnish (FIN) AF: 0.504 AC: 5304 AN: 10514

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.570 AC: 38703 AN: 67928

Other (OTH) AF: 0.543 AC: 1140 AN: 2100

Alfa AF: 0.571 Hom.: 3230

Bravo AF: 0.551

Asia WGS AF: 0.437 AC: 1520 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	1.9
DANN	Benign	0.44
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1217411; hg19: chr1-114356125;