rs13011060

Positions:

• chr2-217073454-G-A
• chr2-217073454-G-C
• chr2-217073454-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.509+79436G>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 0.243 in 152,094 control chromosomes in the GnomAD database, including 4,838 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 0.24 (4838 hom., cov: 31)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP-AS1	XR_001739169.1	n.11844+79436G>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+79436G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.172+79436G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36858 AN: 151976 Hom.: 4826 Cov.: 31

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.0763

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.243 AC: 36894 AN: 152094 Hom.: 4838 Cov.: 31 AF XY: 0.235 AC XY: 17441 AN XY: 74370

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.0761

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.248

Alfa AF: 0.214 Hom.: 2370

Bravo AF: 0.249

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13011060; hg19: chr2-217938177;