Variant 16-55710735-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 0.334 in 152,064 control chromosomes in the GnomAD database, including 11,692 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 0.33 ( 11692 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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:

0.333

AC:

50627

AN:

151944

Hom.:

11650

Cov.:

show subpopulations

Gnomad AFR

AF:

0.658

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.437

Gnomad FIN

AF:

0.220

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.183

Gnomad OTH

AF:

0.307

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

GnomAD4 genome

AF:

0.334

AC:

50716

AN:

152064

Hom.:

11692

Cov.:

AF XY:

0.335

AC XY:

24900

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.658

Gnomad4 AMR

AF:

0.221

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.248

Gnomad4 SAS

AF:

0.437

Gnomad4 FIN

AF:

0.220

Gnomad4 NFE

AF:

0.183

Gnomad4 OTH

AF:

0.307

Alfa

AF:

0.260

Hom.:

2438

Bravo

AF:

0.344

Asia WGS

AF:

0.384

AC:

1335

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.46

DANN

Benign

0.76

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