Variant chr16-11243864-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 0.34 in 152,054 control chromosomes in the GnomAD database, including 9,440 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 0.34 ( 9440 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.956

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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.413 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:

0.341

AC:

51737

AN:

151934

Hom.:

9440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.421

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.334

Gnomad NFE

AF:

0.414

Gnomad OTH

AF:

0.349

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

GnomAD4 genome

AF:

0.340

AC:

51747

AN:

152054

Hom.:

9440

Cov.:

AF XY:

0.339

AC XY:

25179

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.269

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.305

Gnomad4 SAS

AF:

0.429

Gnomad4 FIN

AF:

0.408

Gnomad4 NFE

AF:

0.414

Gnomad4 OTH

AF:

0.351

Alfa

AF:

0.397

Hom.:

13658

Bravo

AF:

0.326

Asia WGS

AF:

0.333

AC:

1158

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.0

DANN

Benign

0.46

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