2-217119937-G-A

Position:

• chr2-217119937-G-A

Variant summary

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

The ENST00000695932.1(DIRC3-AS1):​n.509+125919G>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 151,956 control chromosomes in the GnomAD database, including 10,054 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 (10054 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGFBP-AS1	XR_001739169.1	n.11845-39071G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+125919G>A		intron_variant, non_coding_transcript_variant
DIRC3-AS1	ENST00000695934.1	n.173-33474G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36890 AN: 151838 Hom.: 10017 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.243 AC: 36992 AN: 151956 Hom.: 10054 Cov.: 32 AF XY: 0.240 AC XY: 17859 AN XY: 74288

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.201

Alfa AF: 0.0744 Hom.: 1695

Bravo AF: 0.277

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10173363; hg19: chr2-217984660;