rs1882421

chr2-216985694-T-C

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):n.449-8264T>C 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 0.386 in 152,132 control chromosomes in the GnomAD database, including 14,882 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 0.39 (14882 hom., cov: 33)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP-AS1	XR_001739169.1	n.11784-8264T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.449-8264T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58613 AN: 152016 Hom.: 14840 Cov.: 33

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.0538

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.386 AC: 58689 AN: 152132 Hom.: 14882 Cov.: 33 AF XY: 0.383 AC XY: 28469 AN XY: 74374

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.0534

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.346

Alfa AF: 0.282 Hom.: 9841

Bravo AF: 0.391

Asia WGS AF: 0.185 AC: 646 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.1
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1882421; hg19: chr2-217850417;