Variant chr5-129396979-A-G 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 0.328 in 152,320 control chromosomes in the GnomAD database, including 9,912 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 0.33 ( 9893 hom., cov: 31)

Exomes 𝑓: 0.31 ( 19 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.140

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=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.417 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:

0.328

AC:

49850

AN:

151858

Hom.:

9888

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0985

Gnomad AMI

AF:

0.503

Gnomad AMR

AF:

0.421

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.518

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.363

GnomAD4 exome

AF:

0.314

AC:

108

AN:

344

Hom.:

AF XY:

0.300

AC XY:

AN XY:

190

show subpopulations

Gnomad4 AFR exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.375

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.417

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.328

AC:

49860

AN:

151976

Hom.:

9893

Cov.:

AF XY:

0.333

AC XY:

24701

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.0984

Gnomad4 AMR

AF:

0.421

Gnomad4 ASJ

AF:

0.383

Gnomad4 EAS

AF:

0.221

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.518

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.358

Alfa

AF:

0.390

Hom.:

12559

Bravo

AF:

0.313

Asia WGS

AF:

0.242

AC:

845

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.0

DANN

Benign

0.32

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