2-217526740-C-A

Variant names:

• chr2-217526740-C-A
• rs750365
• ENST00000474063.5:n.322-48182G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000474063.5(DIRC3):​n.322-48182G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,002 control chromosomes in the GnomAD database, including 23,836 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 0.53 (23836 hom., cov: 32)
• Consequence: DIRC3 ENST00000474063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 4 publications found

Genes affected

DIRC3 (HGNC:17805): (disrupted in renal carcinoma 3)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000474063.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIRC3	NR_026597.2		n.1345-48182G>T		intron	N/A
	DIRC3	NR_186292.1		n.2584-48182G>T		intron	N/A
	DIRC3	NR_186293.1		n.1639-14548G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIRC3	ENST00000474063.5	TSL:2	n.322-48182G>T		intron	N/A
	DIRC3	ENST00000486365.6	TSL:5	n.1345-48182G>T		intron	N/A
	DIRC3	ENST00000663562.1		n.1432-48182G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80407 AN: 151884 Hom.: 23794 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.530 AC: 80507 AN: 152002 Hom.: 23836 Cov.: 32 AF XY: 0.534 AC XY: 39642 AN XY: 74302

African (AFR) AF: 0.775 AC: 32147 AN: 41478

American (AMR) AF: 0.548 AC: 8365 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3464

East Asian (EAS) AF: 0.738 AC: 3804 AN: 5154

South Asian (SAS) AF: 0.694 AC: 3341 AN: 4812

European-Finnish (FIN) AF: 0.414 AC: 4370 AN: 10568

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25363 AN: 67944

Other (OTH) AF: 0.497 AC: 1046 AN: 2106

Alfa AF: 0.409 Hom.: 11193

Bravo AF: 0.551

Asia WGS AF: 0.719 AC: 2500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.057
DANN	Benign	0.30
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs750365; hg19: chr2-218391463;