rs2244235

Positions:

• chr2-216968676-C-T

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.449-25282C>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 0.667 in 152,068 control chromosomes in the GnomAD database, including 34,900 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 0.67 (34900 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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 (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGFBP-AS1	XR_001739169.1	n.11784-25282C>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.449-25282C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101324 AN: 151950 Hom.: 34853 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.667 AC: 101425 AN: 152068 Hom.: 34900 Cov.: 31 AF XY: 0.663 AC XY: 49241 AN XY: 74302

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.663

Alfa AF: 0.638 Hom.: 4082

Bravo AF: 0.679

Asia WGS AF: 0.658 AC: 2288 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	1.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244235; hg19: chr2-217833399;