dbSNP rs7576189: DIRC3:n.547-18590G>A (chr2-217758165-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_186293.1(DIRC3):n.547-18590G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 152,174 control chromosomes in the GnomAD database, including 67,000 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 0.94 ( 67000 hom., cov: 30)

Consequence

DIRC3
NR_186293.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.182

Publications

3 publications found

Variant links:

Genes affected

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

DIRC3 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
DIRC3	NR_186293.1 link	n.547-18590G>A	intron_variant	Intron 3 of 16
DIRC3	NR_186296.1 link	n.476+24341G>A	intron_variant	Intron 2 of 13
DIRC3	NR_186298.1 link	n.476+24341G>A	intron_variant	Intron 2 of 13
DIRC3	NR_186301.1 link	n.476+24341G>A	intron_variant	Intron 2 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.938

AC:

142608

AN:

152056

Hom.:

66953

Cov.:

show subpopulations

Gnomad AFR

AF:

0.910

Gnomad AMI

AF:

0.818

Gnomad AMR

AF:

0.954

Gnomad ASJ

AF:

0.925

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.961

Gnomad FIN

AF:

0.965

Gnomad MID

AF:

0.924

Gnomad NFE

AF:

0.943

Gnomad OTH

AF:

0.940

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

GnomAD4 genome

AF:

0.938

AC:

142713

AN:

152174

Hom.:

67000

Cov.:

AF XY:

0.941

AC XY:

69971

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.910

AC:

37751

AN:

41492

American (AMR)

AF:

0.955

AC:

14591

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.925

AC:

3210

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5175

AN:

5176

South Asian (SAS)

AF:

0.961

AC:

4626

AN:

4814

European-Finnish (FIN)

AF:

0.965

AC:

10232

AN:

10606

Middle Eastern (MID)

AF:

0.922

AC:

271

AN:

294

European-Non Finnish (NFE)

AF:

0.943

AC:

64124

AN:

68010

Other (OTH)

AF:

0.941

AC:

1989

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

439

878

1317

1756

2195

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.944

Hom.:

10413

Bravo

AF:

0.934

Asia WGS

AF:

0.976

AC:

3394

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.88

(source)

DANN

Benign

0.76

PhyloP100

-0.18

Splicing

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

Publications

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rs7576189

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over