Variant 1-152566917-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 0.181 in 152,122 control chromosomes in the GnomAD database, including 3,170 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 0.18 ( 3167 hom., cov: 32)

Exomes 𝑓: 0.20 ( 3 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.197

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 (NFE) allele frequency at 95% confidence interval = 0.256 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:

0.181

AC:

27479

AN:

151886

Hom.:

3168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0788

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.0299

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.283

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.259

Gnomad OTH

AF:

0.158

GnomAD4 exome

AF:

0.203

AC:

AN:

118

Hom.:

AF XY:

0.203

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.200

Gnomad4 OTH exome

AF:

0.750

GnomAD4 genome

AF:

0.181

AC:

27478

AN:

152004

Hom.:

3167

Cov.:

AF XY:

0.179

AC XY:

13272

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.0787

Gnomad4 AMR

AF:

0.133

Gnomad4 ASJ

AF:

0.120

Gnomad4 EAS

AF:

0.0301

Gnomad4 SAS

AF:

0.112

Gnomad4 FIN

AF:

0.283

Gnomad4 NFE

AF:

0.259

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.221

Hom.:

5680

Bravo

AF:

0.163

Asia WGS

AF:

0.0710

AC:

249

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

1.9

DANN

Benign

0.56

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