Variant chr3-160740227-C-A 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 0.314 in 152,036 control chromosomes in the GnomAD database, including 7,667 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 0.31 ( 7667 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0470

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 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:

0.315

AC:

47788

AN:

151918

Hom.:

7665

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.506

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.299

Gnomad OTH

AF:

0.257

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

GnomAD4 genome

AF:

0.314

AC:

47811

AN:

152036

Hom.:

7667

Cov.:

AF XY:

0.313

AC XY:

23231

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.345

Gnomad4 AMR

AF:

0.310

Gnomad4 ASJ

AF:

0.197

Gnomad4 EAS

AF:

0.506

Gnomad4 SAS

AF:

0.251

Gnomad4 FIN

AF:

0.289

Gnomad4 NFE

AF:

0.299

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.278

Hom.:

3034

Bravo

AF:

0.319

Asia WGS

AF:

0.322

AC:

1118

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.8

DANN

Benign

0.74

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