Variant 17-18363661-G-C 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 0.665 in 152,246 control chromosomes in the GnomAD database, including 34,005 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 0.66 ( 33990 hom., cov: 35)

Exomes 𝑓: 0.72 ( 15 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.02

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.664

AC:

101044

AN:

152070

Hom.:

33944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.754

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.660

Gnomad ASJ

AF:

0.676

Gnomad EAS

AF:

0.534

Gnomad SAS

AF:

0.522

Gnomad FIN

AF:

0.652

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.635

Gnomad OTH

AF:

0.657

GnomAD4 exome

AF:

0.724

AC:

AN:

Hom.:

AF XY:

0.729

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.700

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.665

AC:

101157

AN:

152188

Hom.:

33990

Cov.:

AF XY:

0.661

AC XY:

49211

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.754

Gnomad4 AMR

AF:

0.660

Gnomad4 ASJ

AF:

0.676

Gnomad4 EAS

AF:

0.535

Gnomad4 SAS

AF:

0.523

Gnomad4 FIN

AF:

0.652

Gnomad4 NFE

AF:

0.635

Gnomad4 OTH

AF:

0.655

Alfa

AF:

0.659

Hom.:

4126

Bravo

AF:

0.668

Asia WGS

AF:

0.511

AC:

1780

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.14

DANN

Benign

0.29

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