Variant 6-160313432-T-C 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 0.462 in 151,786 control chromosomes in the GnomAD database, including 16,676 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 0.46 ( 16676 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.936

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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 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:

0.462

AC:

70103

AN:

151666

Hom.:

16663

Cov.:

show subpopulations

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.431

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.489

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

GnomAD4 genome

AF:

0.462

AC:

70165

AN:

151786

Hom.:

16676

Cov.:

AF XY:

0.462

AC XY:

34291

AN XY:

74182

show subpopulations

Gnomad4 AFR

AF:

0.363

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.555

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.411

Gnomad4 FIN

AF:

0.527

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.486

Alfa

AF:

0.512

Hom.:

4662

Bravo

AF:

0.457

Asia WGS

AF:

0.351

AC:

1220

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.3

DANN

Benign

0.66

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