Genetic Variant DIRC3-AS1:n.509+4740C>G (chr2-216998758-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000695932.1(DIRC3-AS1):n.509+4740C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,064 control chromosomes in the GnomAD database, including 6,615 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 0.25 ( 6615 hom., cov: 32)

Consequence

DIRC3-AS1
ENST00000695932.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0140

Variant links:

Genes affected

DIRC3-AS1 (HGNC:):

DIRC3-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
DIRC3-AS1	ENST00000695932.1 link	n.509+4740C>G	intron_variant	Intron 3 of 11
DIRC3-AS1	ENST00000695934.1 link	n.172+4740C>G	intron_variant	Intron 3 of 8
DIRC3-AS1	ENST00000695937.1 link	n.221+4740C>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38447

AN:

151946

Hom.:

6604

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.336

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.256

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

GnomAD4 genome

AF:

0.253

AC:

38474

AN:

152064

Hom.:

6615

Cov.:

AF XY:

0.261

AC XY:

19368

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.391

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.834

Gnomad4 SAS

AF:

0.276

Gnomad4 FIN

AF:

0.336

Gnomad4 NFE

AF:

0.262

Gnomad4 OTH

AF:

0.258

Alfa

AF:

0.145

Hom.:

305

Bravo

AF:

0.257

Asia WGS

AF:

0.559

AC:

1939

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.1

DANN

Benign

0.49

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over