Variant 8-139321079-G-T 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 0.581 in 151,814 control chromosomes in the GnomAD database, including 25,708 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 0.58 ( 25708 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.41

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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:

0.581

AC:

88159

AN:

151698

Hom.:

25691

Cov.:

show subpopulations

Gnomad AFR

AF:

0.586

Gnomad AMI

AF:

0.579

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.552

Gnomad EAS

AF:

0.497

Gnomad SAS

AF:

0.582

Gnomad FIN

AF:

0.606

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.594

Gnomad OTH

AF:

0.552

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

GnomAD4 genome

AF:

0.581

AC:

88224

AN:

151814

Hom.:

25708

Cov.:

AF XY:

0.580

AC XY:

43033

AN XY:

74176

show subpopulations

Gnomad4 AFR

AF:

0.586

Gnomad4 AMR

AF:

0.535

Gnomad4 ASJ

AF:

0.552

Gnomad4 EAS

AF:

0.497

Gnomad4 SAS

AF:

0.584

Gnomad4 FIN

AF:

0.606

Gnomad4 NFE

AF:

0.594

Gnomad4 OTH

AF:

0.552

Alfa

AF:

0.585

Hom.:

51944

Bravo

AF:

0.573

Asia WGS

AF:

0.537

AC:

1869

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.3

DANN

Benign

0.47

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