Variant 6-31815431-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.429 in 596,576 control chromosomes in the GnomAD database, including 59,283 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.51 ( 21347 hom., cov: 31)

Exomes 𝑓: 0.40 ( 37936 hom. )

Consequence

Unknown

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.162

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 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:

0.507

AC:

76984

AN:

151764

Hom.:

21320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.743

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.493

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.386

Gnomad OTH

AF:

0.516

GnomAD4 exome

AF:

0.402

AC:

178819

AN:

444694

Hom.:

37936

Cov.:

AF XY:

0.401

AC XY:

94639

AN XY:

235736

show subpopulations

Gnomad4 AFR exome

AF:

0.740

Gnomad4 AMR exome

AF:

0.474

Gnomad4 ASJ exome

AF:

0.381

Gnomad4 EAS exome

AF:

0.411

Gnomad4 SAS exome

AF:

0.459

Gnomad4 FIN exome

AF:

0.475

Gnomad4 NFE exome

AF:

0.363

Gnomad4 OTH exome

AF:

0.434

GnomAD4 genome

AF:

0.507

AC:

77056

AN:

151882

Hom.:

21347

Cov.:

AF XY:

0.509

AC XY:

37810

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.743

Gnomad4 AMR

AF:

0.498

Gnomad4 ASJ

AF:

0.378

Gnomad4 EAS

AF:

0.414

Gnomad4 SAS

AF:

0.484

Gnomad4 FIN

AF:

0.493

Gnomad4 NFE

AF:

0.386

Gnomad4 OTH

AF:

0.517

Alfa

AF:

0.255

Hom.:

512

Bravo

AF:

0.518

Asia WGS

AF:

0.550

AC:

1910

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Chronic obstructive pulmonary disease

Other:1

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Aug 04, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

DANN

Benign

0.84

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over