Variant chr4-39669522-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 0.3 in 151,994 control chromosomes in the GnomAD database, including 8,157 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 0.30 ( 8157 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.00

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=-0.76).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.456 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:

0.300

AC:

45557

AN:

151876

Hom.:

8146

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.464

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.407

Gnomad SAS

AF:

0.376

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.371

Gnomad OTH

AF:

0.354

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

GnomAD4 genome

AF:

0.300

AC:

45575

AN:

151994

Hom.:

8157

Cov.:

AF XY:

0.298

AC XY:

22126

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.100

Gnomad4 AMR

AF:

0.465

Gnomad4 ASJ

AF:

0.330

Gnomad4 EAS

AF:

0.407

Gnomad4 SAS

AF:

0.376

Gnomad4 FIN

AF:

0.273

Gnomad4 NFE

AF:

0.371

Gnomad4 OTH

AF:

0.353

Alfa

AF:

0.361

Hom.:

17665

Bravo

AF:

0.304

Asia WGS

AF:

0.386

AC:

1342

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.85

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