rs16857609

Variant names:

• chr2-217431785-C-T
• rs16857609
• ENST00000474063.5:n.958+1138G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000474063.5(DIRC3):​n.958+1138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,048 control chromosomes in the GnomAD database, including 6,747 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 0.28 (6747 hom., cov: 31)
• Consequence: DIRC3 ENST00000474063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 86 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIRC3	NR_026597.2		n.1790+1138G>A		intron	N/A
	DIRC3	NR_186292.1		n.3029+1138G>A		intron	N/A
	DIRC3	NR_186293.1		n.2234+1138G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIRC3	ENST00000474063.5	TSL:2	n.958+1138G>A		intron	N/A
	DIRC3	ENST00000484635.1	TSL:5	n.368+1138G>A		intron	N/A
	DIRC3	ENST00000486365.6	TSL:5	n.1790+1138G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43050 AN: 151930 Hom.: 6734 Cov.: 31

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.283 AC: 43099 AN: 152048 Hom.: 6747 Cov.: 31 AF XY: 0.290 AC XY: 21543 AN XY: 74312

African (AFR) AF: 0.238 AC: 9876 AN: 41472

American (AMR) AF: 0.328 AC: 5020 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3472

East Asian (EAS) AF: 0.595 AC: 3055 AN: 5134

South Asian (SAS) AF: 0.550 AC: 2642 AN: 4804

European-Finnish (FIN) AF: 0.300 AC: 3179 AN: 10584

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17449 AN: 67980

Other (OTH) AF: 0.279 AC: 589 AN: 2112

Alfa AF: 0.271 Hom.: 10448

Bravo AF: 0.284

Asia WGS AF: 0.555 AC: 1932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.87
PhyloP100		0.34

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs16857609;

hg19: chr2-218296508;