2-217030033-T-C

Position:

• chr2-217030033-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.509+36015T>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 0.341 in 151,956 control chromosomes in the GnomAD database, including 9,901 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 (9901 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP-AS1	XR_001739169.1	n.11844+36015T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+36015T>C		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.172+36015T>C		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695937.1	n.222-7180T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51776 AN: 151838 Hom.: 9885 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.341 AC: 51828 AN: 151956 Hom.: 9901 Cov.: 32 AF XY: 0.348 AC XY: 25833 AN XY: 74272

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.338

Alfa AF: 0.293 Hom.: 15054

Bravo AF: 0.354

Asia WGS AF: 0.614 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4491709; hg19: chr2-217894756;