Variant chr6-42206740-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 0.678 in 152,112 control chromosomes in the GnomAD database, including 35,486 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 0.68 ( 35484 hom., cov: 32)

Exomes 𝑓: 0.83 ( 2 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0810

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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 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:

0.677

AC:

102953

AN:

151988

Hom.:

35441

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.717

Gnomad AMR

AF:

0.729

Gnomad ASJ

AF:

0.648

Gnomad EAS

AF:

0.916

Gnomad SAS

AF:

0.766

Gnomad FIN

AF:

0.783

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.695

Gnomad OTH

AF:

0.677

GnomAD4 exome

AF:

0.833

AC:

AN:

Hom.:

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

1.00

GnomAD4 genome

AF:

0.678

AC:

103053

AN:

152106

Hom.:

35484

Cov.:

AF XY:

0.684

AC XY:

50883

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.564

Gnomad4 AMR

AF:

0.730

Gnomad4 ASJ

AF:

0.648

Gnomad4 EAS

AF:

0.917

Gnomad4 SAS

AF:

0.767

Gnomad4 FIN

AF:

0.783

Gnomad4 NFE

AF:

0.695

Gnomad4 OTH

AF:

0.681

Alfa

AF:

0.689

Hom.:

34895

Bravo

AF:

0.674

Asia WGS

AF:

0.823

AC:

2860

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.87

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