rs13020935

chr2-216760956-G-Achr2-216760956-G-Cchr2-216760956-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.448+48487G>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 0.645 in 152,014 control chromosomes in the GnomAD database, including 32,410 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 0.64 (32410 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGFBP-AS1	XR_001739169.1	n.482-3933G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.448+48487G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000447289.1	n.389-3933G>A		intron_variant, non_coding_transcript_variant		5
DIRC3-AS1	ENST00000695934.1	n.111+48487G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000702642.1	n.324-38593G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97974 AN: 151896 Hom.: 32390 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.645 AC: 98029 AN: 152014 Hom.: 32410 Cov.: 32 AF XY: 0.640 AC XY: 47556 AN XY: 74284

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.688

Alfa AF: 0.702 Hom.: 14917

Bravo AF: 0.643

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	7.1
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: rs13020935; hg19: chr2-217625679;