rs1882420

Positions:

• chr2-216986786-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.449-7172G>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 0.299 in 152,046 control chromosomes in the GnomAD database, including 11,291 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 0.30 (11291 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGFBP-AS1	XR_001739169.1	n.11784-7172G>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.449-7172G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45352 AN: 151928 Hom.: 11249 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.299 AC: 45453 AN: 152046 Hom.: 11291 Cov.: 32 AF XY: 0.300 AC XY: 22262 AN XY: 74312

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.254

Alfa AF: 0.147 Hom.: 3440

Bravo AF: 0.322

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
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: rs1882420; hg19: chr2-217851509;