Variant chr5-132534997-T-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 0.378 in 152,008 control chromosomes in the GnomAD database, including 11,476 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 0.38 ( 11476 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0780

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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:

0.378

AC:

57382

AN:

151890

Hom.:

11462

Cov.:

show subpopulations

Gnomad AFR

AF:

0.454

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.692

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.414

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

GnomAD4 genome

AF:

0.378

AC:

57434

AN:

152008

Hom.:

11476

Cov.:

AF XY:

0.375

AC XY:

27844

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.454

Gnomad4 AMR

AF:

0.350

Gnomad4 ASJ

AF:

0.375

Gnomad4 EAS

AF:

0.692

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.276

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.416

Alfa

AF:

0.355

Hom.:

14491

Bravo

AF:

0.394

Asia WGS

AF:

0.512

AC:

1780

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.4

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