Variant chr3-180227563-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 0.287 in 152,114 control chromosomes in the GnomAD database, including 6,491 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 0.29 ( 6491 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.154

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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.287

AC:

43629

AN:

151996

Hom.:

6483

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.349

Gnomad ASJ

AF:

0.207

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.478

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.287

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

GnomAD4 genome

AF:

0.287

AC:

43671

AN:

152114

Hom.:

6491

Cov.:

AF XY:

0.294

AC XY:

21838

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.331

Gnomad4 AMR

AF:

0.350

Gnomad4 ASJ

AF:

0.207

Gnomad4 EAS

AF:

0.381

Gnomad4 SAS

AF:

0.478

Gnomad4 FIN

AF:

0.251

Gnomad4 NFE

AF:

0.235

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.251

Hom.:

5904

Bravo

AF:

0.292

Asia WGS

AF:

0.438

AC:

1526

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.1

DANN

Benign

0.73

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