rs13016130

Positions:

• chr2-217109554-G-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+115536G>T 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 0.343 in 151,950 control chromosomes in the GnomAD database, including 10,794 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 0.34 (10794 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGFBP-AS1	XR_001739169.1	n.11845-49454G>T		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+115536G>T		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.173-43857G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52163 AN: 151830 Hom.: 10790 Cov.: 31

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.343 AC: 52173 AN: 151950 Hom.: 10794 Cov.: 31 AF XY: 0.347 AC XY: 25760 AN XY: 74236

Gnomad4 AFR AF: 0.0974

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.369

Alfa AF: 0.395 Hom.: 1754

Bravo AF: 0.336

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.80
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: rs13016130; hg19: chr2-217974277;