rs13013872

Positions:

• chr2-217091812-A-G
• chr2-217091812-A-T

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.509+97794A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 148,878 control chromosomes in the GnomAD database, including 30,594 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 0.61 (30594 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

DIRC3-AS1 (HGNC:50636): (DIRC3 antisense RNA 1)

IGFBP-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGFBP-AS1	XR_001739169.1	n.11845-67196A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+97794A>G		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.173-61599A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.614 AC: 91287 AN: 148762 Hom.: 30551 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.614 AC: 91389 AN: 148878 Hom.: 30594 Cov.: 31 AF XY: 0.608 AC XY: 44222 AN XY: 72760

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.605

Alfa AF: 0.590 Hom.: 4732

Bravo AF: 0.639

Asia WGS AF: 0.517 AC: 1798 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13013872; hg19: chr2-217956535;