rs10209401

Variant names:

• chr2-217339958-A-C
• rs10209401
• ENST00000474063.5:n.1459-11806T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-217339958-A-C
• chr2-217339958-A-T

Variant summary

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

The ENST00000474063.5(DIRC3):​n.1459-11806T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,072 control chromosomes in the GnomAD database, including 46,623 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 0.76 (46623 hom., cov: 30)
• Consequence: DIRC3 ENST00000474063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669
• Publications: 3 publications found

Genes affected

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

DIRC3-AS1 (HGNC:50636): (DIRC3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 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.2291-11806T>G		intron	N/A
	DIRC3-AS1	NR_133642.1		n.1024+3377A>C		intron	N/A
	DIRC3	NR_186292.1		n.3530-11806T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DIRC3	ENST00000474063.5	TSL:2	n.1459-11806T>G		intron	N/A
	DIRC3	ENST00000486365.6	TSL:5	n.2291-11806T>G		intron	N/A
	DIRC3	ENST00000663562.1		n.2378-11806T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116089 AN: 151954 Hom.: 46613 Cov.: 30

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.764 AC: 116133 AN: 152072 Hom.: 46623 Cov.: 30 AF XY: 0.766 AC XY: 56918 AN XY: 74334

African (AFR) AF: 0.498 AC: 20646 AN: 41438

American (AMR) AF: 0.792 AC: 12107 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3081 AN: 3470

East Asian (EAS) AF: 0.737 AC: 3797 AN: 5154

South Asian (SAS) AF: 0.719 AC: 3454 AN: 4804

European-Finnish (FIN) AF: 0.915 AC: 9689 AN: 10592

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60611 AN: 68020

Other (OTH) AF: 0.791 AC: 1670 AN: 2110

Alfa AF: 0.845 Hom.: 170573

Bravo AF: 0.740

Asia WGS AF: 0.681 AC: 2371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.67
PhyloP100		0.67

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: rs10209401;

hg19: chr2-218204681;