Variant 6-80939927-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 0.514 in 151,974 control chromosomes in the GnomAD database, including 20,766 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 0.51 ( 20766 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.931

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 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:

0.514

AC:

78031

AN:

151856

Hom.:

20710

Cov.:

show subpopulations

Gnomad AFR

AF:

0.640

Gnomad AMI

AF:

0.446

Gnomad AMR

AF:

0.480

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.702

Gnomad SAS

AF:

0.609

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.442

Gnomad NFE

AF:

0.436

Gnomad OTH

AF:

0.500

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

GnomAD4 genome

AF:

0.514

AC:

78140

AN:

151974

Hom.:

20766

Cov.:

AF XY:

0.519

AC XY:

38539

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.641

Gnomad4 AMR

AF:

0.480

Gnomad4 ASJ

AF:

0.481

Gnomad4 EAS

AF:

0.702

Gnomad4 SAS

AF:

0.608

Gnomad4 FIN

AF:

0.458

Gnomad4 NFE

AF:

0.436

Gnomad4 OTH

AF:

0.506

Alfa

AF:

0.465

Hom.:

8484

Bravo

AF:

0.519

Asia WGS

AF:

0.666

AC:

2316

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.15

DANN

Benign

0.22

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