rs6739040

chr2-217087003-A-Gchr2-217087003-A-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+92985A>G 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 0.12 in 152,210 control chromosomes in the GnomAD database, including 1,548 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 0.12 (1548 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP-AS1	XR_001739169.1	n.11845-72005A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+92985A>G		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.173-66408A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18172 AN: 152092 Hom.: 1544 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.0885

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0718

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.120 AC: 18207 AN: 152210 Hom.: 1548 Cov.: 32 AF XY: 0.117 AC XY: 8697 AN XY: 74420

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.0974

Gnomad4 ASJ AF: 0.0885

Gnomad4 EAS AF: 0.0261

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0718

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0821 Hom.: 923

Bravo AF: 0.127

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	1.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6739040; hg19: chr2-217951726;