Variant 16-79957119-T-G 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 0.752 in 152,038 control chromosomes in the GnomAD database, including 43,270 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 0.75 ( 43270 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.859

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=-0.97).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.81 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:

0.752

AC:

114198

AN:

151920

Hom.:

43239

Cov.:

show subpopulations

Gnomad AFR

AF:

0.668

Gnomad AMI

AF:

0.741

Gnomad AMR

AF:

0.821

Gnomad ASJ

AF:

0.843

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.825

Gnomad FIN

AF:

0.778

Gnomad MID

AF:

0.826

Gnomad NFE

AF:

0.782

Gnomad OTH

AF:

0.778

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

GnomAD4 genome

AF:

0.752

AC:

114284

AN:

152038

Hom.:

43270

Cov.:

AF XY:

0.752

AC XY:

55908

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.668

Gnomad4 AMR

AF:

0.822

Gnomad4 ASJ

AF:

0.843

Gnomad4 EAS

AF:

0.613

Gnomad4 SAS

AF:

0.826

Gnomad4 FIN

AF:

0.778

Gnomad4 NFE

AF:

0.782

Gnomad4 OTH

AF:

0.778

Alfa

AF:

0.779

Hom.:

12305

Bravo

AF:

0.750

Asia WGS

AF:

0.726

AC:

2523

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.13

DANN

Benign

0.49

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