rs12466929

Variant names:

• chr2-217115710-G-A
• rs12466929
• ENST00000695932.1:n.509+121692G>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+121692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,886 control chromosomes in the GnomAD database, including 3,794 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 0.20 (3794 hom., cov: 32)
• Consequence: DIRC3-AS1 ENST00000695932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

DIRC3-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 (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIRC3-AS1	ENST00000695932.1	n.509+121692G>A		intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1	n.173-37701G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29867 AN: 151768 Hom.: 3786 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.197 AC: 29904 AN: 151886 Hom.: 3794 Cov.: 32 AF XY: 0.205 AC XY: 15226 AN XY: 74244

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.182

Alfa AF: 0.124 Hom.: 2180

Bravo AF: 0.205

Asia WGS AF: 0.350 AC: 1216 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	0.55
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12466929; hg19: chr2-217980433;