Variant 5-111217704-A-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 0.381 in 151,794 control chromosomes in the GnomAD database, including 11,296 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 0.38 ( 11296 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.594

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 (SAS) allele frequency at 95% confidence interval = 0.453 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:

0.381

AC:

57841

AN:

151676

Hom.:

11298

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.371

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.198

Gnomad SAS

AF:

0.460

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.352

Gnomad OTH

AF:

0.357

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

GnomAD4 genome

AF:

0.381

AC:

57864

AN:

151794

Hom.:

11296

Cov.:

AF XY:

0.383

AC XY:

28432

AN XY:

74174

show subpopulations

Gnomad4 AFR

AF:

0.458

Gnomad4 AMR

AF:

0.371

Gnomad4 ASJ

AF:

0.313

Gnomad4 EAS

AF:

0.197

Gnomad4 SAS

AF:

0.460

Gnomad4 FIN

AF:

0.370

Gnomad4 NFE

AF:

0.352

Gnomad4 OTH

AF:

0.358

Alfa

AF:

0.348

Hom.:

12622

Bravo

AF:

0.379

Asia WGS

AF:

0.330

AC:

1146

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

0.97

DANN

Benign

0.68

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