Variant chr1-114173741-C-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 0.21 in 152,014 control chromosomes in the GnomAD database, including 3,662 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 ( 3662 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.17

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=-0.89).

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	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31897

AN:

151896

Hom.:

3662

Cov.:

show subpopulations

Gnomad AFR

AF:

0.189

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.176

Gnomad ASJ

AF:

0.289

Gnomad EAS

AF:

0.00289

Gnomad SAS

AF:

0.0812

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.216

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

GnomAD4 genome

AF:

0.210

AC:

31909

AN:

152014

Hom.:

3662

Cov.:

AF XY:

0.202

AC XY:

15022

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.189

Gnomad4 AMR

AF:

0.176

Gnomad4 ASJ

AF:

0.289

Gnomad4 EAS

AF:

0.00289

Gnomad4 SAS

AF:

0.0806

Gnomad4 FIN

AF:

0.182

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.214

Alfa

AF:

0.204

Hom.:

1877

Bravo

AF:

0.211

Asia WGS

AF:

0.0560

AC:

196

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.014

DANN

Benign

0.81

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