rs2488457

Variant names:

• chr1-113872746-G-C
• rs2488457
• ENST00000419536.1:n.246+14730G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-113872746-G-C
• chr1-113872746-G-A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000419536.1(AP4B1-AS1):​n.246+14730G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,128 control chromosomes in the GnomAD database, including 51,265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency: Genomes: 𝑓 0.81 (51265 hom., cov: 32)
• Consequence: AP4B1-AS1 ENST00000419536.1 intron
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.196
• Publications: 120 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 1-113872746-G-C is Benign according to our data. Variant chr1-113872746-G-C is described in ClinVar as Benign. ClinVar VariationId is 8910.Status of the report is no_assertion_criteria_provided, 0 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AP4B1-AS1	NR_037864.1		n.246+14730G>C		intron	N/A
	AP4B1-AS1	NR_125965.1		n.415-25122G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AP4B1-AS1	ENST00000419536.1	TSL:2	n.246+14730G>C		intron	N/A
	AP4B1-AS1	ENST00000717022.1		n.441-22414G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123506 AN: 152010 Hom.: 51201 Cov.: 32

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.813 AC: 123632 AN: 152128 Hom.: 51265 Cov.: 32 AF XY: 0.806 AC XY: 59937 AN XY: 74338

African (AFR) AF: 0.958 AC: 39815 AN: 41554

American (AMR) AF: 0.739 AC: 11281 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2777 AN: 3466

East Asian (EAS) AF: 0.395 AC: 2040 AN: 5162

South Asian (SAS) AF: 0.814 AC: 3923 AN: 4818

European-Finnish (FIN) AF: 0.693 AC: 7304 AN: 10540

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53792 AN: 67992

Other (OTH) AF: 0.789 AC: 1670 AN: 2116

Alfa AF: 0.797 Hom.: 5716

Bravo AF: 0.813

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	Diabetes mellitus, insulin-dependent, susceptibility to (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2488457; hg19: chr1-114415368;