Variant chr6-32622686-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 0.274 in 151,868 control chromosomes in the GnomAD database, including 6,080 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 0.27 ( 6080 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.185

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 (EAS) allele frequency at 95% confidence interval = 0.338 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:

0.274

AC:

41636

AN:

151750

Hom.:

6077

Cov.:

show subpopulations

Gnomad AFR

AF:

0.203

Gnomad AMI

AF:

0.416

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.329

Gnomad EAS

AF:

0.350

Gnomad SAS

AF:

0.256

Gnomad FIN

AF:

0.241

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.303

Gnomad OTH

AF:

0.274

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

GnomAD4 genome

AF:

0.274

AC:

41667

AN:

151868

Hom.:

6080

Cov.:

AF XY:

0.272

AC XY:

20169

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.203

Gnomad4 AMR

AF:

0.325

Gnomad4 ASJ

AF:

0.329

Gnomad4 EAS

AF:

0.351

Gnomad4 SAS

AF:

0.255

Gnomad4 FIN

AF:

0.241

Gnomad4 NFE

AF:

0.303

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.264

Hom.:

623

Bravo

AF:

0.285

Asia WGS

AF:

0.249

AC:

869

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

8.0

DANN

Benign

0.55

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