Variant 1-111017226-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 0.208 in 152,052 control chromosomes in the GnomAD database, including 3,542 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 0.21 ( 3542 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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:

0.208

AC:

31640

AN:

151934

Hom.:

3543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.00404

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.208

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

GnomAD4 genome

AF:

0.208

AC:

31651

AN:

152052

Hom.:

3542

Cov.:

AF XY:

0.204

AC XY:

15137

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.00405

Gnomad4 SAS

AF:

0.170

Gnomad4 FIN

AF:

0.258

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.205

Alfa

AF:

0.234

Hom.:

6248

Bravo

AF:

0.197

Asia WGS

AF:

0.0880

AC:

305

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.0

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