rs13015993

Positions:

• chr2-216760800-G-A
• chr2-216760800-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_187138.1(IGFBP-AS1):​n.407-4089G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,986 control chromosomes in the GnomAD database, including 32,360 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 0.64 (32360 hom., cov: 32)
• Consequence: IGFBP-AS1 NR_187138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563

Genes affected

DIRC3-AS1 (HGNC:):

IGFBP-AS1 (HGNC:55655): (IGFBP5 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGFBP-AS1	NR_187138.1	n.407-4089G>A		intron_variant
IGFBP-AS1	NR_187139.1	n.407-4089G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIRC3-AS1	ENST00000447289.1	n.389-4089G>A		intron_variant		5
DIRC3-AS1	ENST00000695932.1	n.448+48331G>A		intron_variant
DIRC3-AS1	ENST00000695934.1	n.111+48331G>A		intron_variant
DIRC3-AS1	ENST00000702642.1	n.324-38749G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97873 AN: 151866 Hom.: 32340 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.644 AC: 97928 AN: 151986 Hom.: 32360 Cov.: 32 AF XY: 0.640 AC XY: 47501 AN XY: 74262

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.688

Alfa AF: 0.716 Hom.: 63875

Bravo AF: 0.637

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13015993; hg19: chr2-217625523;