rs1382435

Variant names:

• chr2-217431280-T-C
• rs1382435
• ENST00000474063.5:n.958+1643A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-217431280-T-C
• chr2-217431280-T-G

Variant summary

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

The ENST00000474063.5(DIRC3):​n.958+1643A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,772 control chromosomes in the GnomAD database, including 24,005 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 0.54 (24005 hom., cov: 30)
• Consequence: DIRC3 ENST00000474063.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIRC3	NR_026597.2	n.1790+1643A>G		intron_variant	Intron 5 of 12
DIRC3	NR_186292.1	n.3029+1643A>G		intron_variant	Intron 7 of 14
DIRC3	NR_186293.1	n.2234+1643A>G		intron_variant	Intron 9 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIRC3	ENST00000474063.5	n.958+1643A>G		intron_variant	Intron 4 of 11	2
DIRC3	ENST00000484635.1	n.368+1643A>G		intron_variant	Intron 2 of 4	5
DIRC3	ENST00000486365.6	n.1790+1643A>G		intron_variant	Intron 5 of 12	5

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81238 AN: 151654 Hom.: 24004 Cov.: 30

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.535 AC: 81271 AN: 151772 Hom.: 24005 Cov.: 30 AF XY: 0.530 AC XY: 39317 AN XY: 74148

African (AFR) AF: 0.318 AC: 13153 AN: 41342

American (AMR) AF: 0.549 AC: 8355 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2262 AN: 3466

East Asian (EAS) AF: 0.316 AC: 1627 AN: 5154

South Asian (SAS) AF: 0.231 AC: 1110 AN: 4802

European-Finnish (FIN) AF: 0.656 AC: 6917 AN: 10548

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.677 AC: 45972 AN: 67930

Other (OTH) AF: 0.570 AC: 1202 AN: 2108

Alfa AF: 0.619 Hom.: 92948

Bravo AF: 0.522

Asia WGS AF: 0.261 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.55
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1382435; hg19: chr2-218296003;