Variant 16-79627600-C-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 0.769 in 152,160 control chromosomes in the GnomAD database, including 45,442 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 0.77 ( 45442 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0700

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 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:

0.769

AC:

116923

AN:

152042

Hom.:

45410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.710

Gnomad AMI

AF:

0.731

Gnomad AMR

AF:

0.657

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.692

Gnomad SAS

AF:

0.786

Gnomad FIN

AF:

0.870

Gnomad MID

AF:

0.753

Gnomad NFE

AF:

0.823

Gnomad OTH

AF:

0.768

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

GnomAD4 genome

AF:

0.769

AC:

117000

AN:

152160

Hom.:

45442

Cov.:

AF XY:

0.768

AC XY:

57142

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.710

Gnomad4 AMR

AF:

0.656

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.692

Gnomad4 SAS

AF:

0.787

Gnomad4 FIN

AF:

0.870

Gnomad4 NFE

AF:

0.823

Gnomad4 OTH

AF:

0.767

Alfa

AF:

0.750

Hom.:

2655

Bravo

AF:

0.745

Asia WGS

AF:

0.757

AC:

2634

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.6

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