Variant chr6-32792937-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 0.614 in 151,976 control chromosomes in the GnomAD database, including 28,886 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 0.61 ( 28886 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.32792937G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.615

AC:

93317

AN:

151858

Hom.:

28871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.639

Gnomad AMI

AF:

0.750

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.698

Gnomad SAS

AF:

0.712

Gnomad FIN

AF:

0.679

Gnomad MID

AF:

0.637

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.609

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

GnomAD4 genome

AF:

0.614

AC:

93371

AN:

151976

Hom.:

28886

Cov.:

AF XY:

0.620

AC XY:

46031

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.638

Gnomad4 AMR

AF:

0.577

Gnomad4 ASJ

AF:

0.602

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.712

Gnomad4 FIN

AF:

0.679

Gnomad4 NFE

AF:

0.584

Gnomad4 OTH

AF:

0.613

Alfa

AF:

0.565

Hom.:

6310

Bravo

AF:

0.606

Asia WGS

AF:

0.689

AC:

2394

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

2.3

DANN

Benign

0.75

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