Variant chr3-197365786-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 0.128 in 152,134 control chromosomes in the GnomAD database, including 1,761 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 0.13 ( 1761 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17

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=-0.77).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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:

0.128

AC:

19497

AN:

152016

Hom.:

1758

Cov.:

show subpopulations

Gnomad AFR

AF:

0.259

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0928

Gnomad ASJ

AF:

0.0559

Gnomad EAS

AF:

0.0526

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.0600

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.0762

Gnomad OTH

AF:

0.123

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

GnomAD4 genome

AF:

0.128

AC:

19522

AN:

152134

Hom.:

1761

Cov.:

AF XY:

0.127

AC XY:

9422

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.259

Gnomad4 AMR

AF:

0.0927

Gnomad4 ASJ

AF:

0.0559

Gnomad4 EAS

AF:

0.0526

Gnomad4 SAS

AF:

0.135

Gnomad4 FIN

AF:

0.0600

Gnomad4 NFE

AF:

0.0763

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.0844

Hom.:

1146

Bravo

AF:

0.134

Asia WGS

AF:

0.120

AC:

417

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.65

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