Variant chr5-178709004-G-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 0.25 in 152,222 control chromosomes in the GnomAD database, including 5,218 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 0.25 ( 5218 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.668

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 (SAS) allele frequency at 95% confidence interval = 0.379 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:

0.250

AC:

38007

AN:

152104

Hom.:

5213

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.248

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.250

AC:

38038

AN:

152222

Hom.:

5218

Cov.:

AF XY:

0.258

AC XY:

19209

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.138

Gnomad4 AMR

AF:

0.248

Gnomad4 ASJ

AF:

0.285

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.394

Gnomad4 FIN

AF:

0.386

Gnomad4 NFE

AF:

0.281

Gnomad4 OTH

AF:

0.247

Alfa

AF:

0.266

Hom.:

5205

Bravo

AF:

0.230

Asia WGS

AF:

0.371

AC:

1294

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

0.99

DANN

Benign

0.54

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