Variant chr5-179793637-A-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 0.283 in 985,288 control chromosomes in the GnomAD database, including 41,327 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 0.22 ( 4362 hom., cov: 33)

Exomes 𝑓: 0.29 ( 36965 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.63

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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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:

0.218

AC:

33120

AN:

152064

Hom.:

4363

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0829

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.165

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.228

GnomAD4 exome

AF:

0.295

AC:

245618

AN:

833108

Hom.:

36965

Cov.:

AF XY:

0.294

AC XY:

113239

AN XY:

384714

show subpopulations

Gnomad4 AFR exome

AF:

0.0613

Gnomad4 AMR exome

AF:

0.203

Gnomad4 ASJ exome

AF:

0.240

Gnomad4 EAS exome

AF:

0.163

Gnomad4 SAS exome

AF:

0.189

Gnomad4 FIN exome

AF:

0.283

Gnomad4 NFE exome

AF:

0.304

Gnomad4 OTH exome

AF:

0.264

GnomAD4 genome

AF:

0.218

AC:

33129

AN:

152180

Hom.:

4362

Cov.:

AF XY:

0.217

AC XY:

16173

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.0829

Gnomad4 AMR

AF:

0.179

Gnomad4 ASJ

AF:

0.239

Gnomad4 EAS

AF:

0.165

Gnomad4 SAS

AF:

0.188

Gnomad4 FIN

AF:

0.332

Gnomad4 NFE

AF:

0.297

Gnomad4 OTH

AF:

0.225

Alfa

AF:

0.265

Hom.:

7152

Bravo

AF:

0.200

Asia WGS

AF:

0.165

AC:

573

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.0040

DANN

Benign

0.70

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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