rs10169372

chr2-217006626-A-Gchr2-217006626-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+12608A>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 0.0766 in 152,102 control chromosomes in the GnomAD database, including 1,218 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 0.077 (1218 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP-AS1	XR_001739169.1	n.11844+12608A>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+12608A>G		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.172+12608A>G		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695937.1	n.221+12608A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0764 AC: 11619 AN: 151984 Hom.: 1216 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0341

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.00694

Gnomad OTH AF: 0.0586

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

GnomAD4 genome AF: 0.0766 AC: 11650 AN: 152102 Hom.: 1218 Cov.: 32 AF XY: 0.0744 AC XY: 5529 AN XY: 74354

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.0383

Gnomad4 SAS AF: 0.0507

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.00694

Gnomad4 OTH AF: 0.0570

Alfa AF: 0.0285 Hom.: 116

Bravo AF: 0.0859

Asia WGS AF: 0.0510 AC: 178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.2
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10169372; hg19: chr2-217871349;