rs12998806

chr2-217029040-G-A

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):n.509+35022G>A 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 0.179 in 152,144 control chromosomes in the GnomAD database, including 2,682 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 0.18 (2682 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP-AS1	XR_001739169.1	n.11844+35022G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+35022G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.172+35022G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695937.1	n.222-8173G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27261 AN: 152024 Hom.: 2674 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0799

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.179 AC: 27279 AN: 152144 Hom.: 2682 Cov.: 32 AF XY: 0.173 AC XY: 12896 AN XY: 74398

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0799

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.194

Alfa AF: 0.196 Hom.: 893

Bravo AF: 0.181

Asia WGS AF: 0.137 AC: 477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.17
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12998806; hg19: chr2-217893763;