Variant 2-217020936-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.718 in 151,932 control chromosomes in the GnomAD database, including 39,698 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 0.72 ( 39698 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.130

Variant links:

Genes affected

(HGNC:):

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.217020936C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
DIRC3-AS1	ENST00000695932.1 linkuse as main transcript	n.509+26918C>T	intron_variant
DIRC3-AS1	ENST00000695934.1 linkuse as main transcript	n.172+26918C>T	intron_variant
DIRC3-AS1	ENST00000695937.1 linkuse as main transcript	n.222-16277C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

108945

AN:

151814

Hom.:

39647

Cov.:

show subpopulations

Gnomad AFR

AF:

0.825

Gnomad AMI

AF:

0.609

Gnomad AMR

AF:

0.733

Gnomad ASJ

AF:

0.658

Gnomad EAS

AF:

0.934

Gnomad SAS

AF:

0.717

Gnomad FIN

AF:

0.630

Gnomad MID

AF:

0.704

Gnomad NFE

AF:

0.651

Gnomad OTH

AF:

0.697

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

GnomAD4 genome

AF:

0.718

AC:

109053

AN:

151932

Hom.:

39698

Cov.:

AF XY:

0.716

AC XY:

53192

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.825

Gnomad4 AMR

AF:

0.734

Gnomad4 ASJ

AF:

0.658

Gnomad4 EAS

AF:

0.934

Gnomad4 SAS

AF:

0.717

Gnomad4 FIN

AF:

0.630

Gnomad4 NFE

AF:

0.651

Gnomad4 OTH

AF:

0.700

Alfa

AF:

0.660

Hom.:

51712

Bravo

AF:

0.735

Asia WGS

AF:

0.855

AC:

2940

AN:

3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.77

DANN

Benign

0.69

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