Variant chr16-65661448-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 0.302 in 152,020 control chromosomes in the GnomAD database, including 7,822 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 0.30 ( 7822 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.88

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 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:

0.302

AC:

45863

AN:

151902

Hom.:

7811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.468

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.249

Gnomad EAS

AF:

0.0851

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.285

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

GnomAD4 genome

AF:

0.302

AC:

45900

AN:

152020

Hom.:

7822

Cov.:

AF XY:

0.300

AC XY:

22257

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.468

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.249

Gnomad4 EAS

AF:

0.0847

Gnomad4 SAS

AF:

0.270

Gnomad4 FIN

AF:

0.256

Gnomad4 NFE

AF:

0.248

Gnomad4 OTH

AF:

0.282

Alfa

AF:

0.264

Hom.:

2588

Bravo

AF:

0.301

Asia WGS

AF:

0.221

AC:

772

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.0010

DANN

Benign

0.50

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