Variant 1-160108064-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 0.166 in 152,148 control chromosomes in the GnomAD database, including 2,409 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 0.17 ( 2409 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.439

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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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:

0.166

AC:

25277

AN:

152030

Hom.:

2401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.324

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.198

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

GnomAD4 genome

AF:

0.166

AC:

25310

AN:

152148

Hom.:

2409

Cov.:

AF XY:

0.170

AC XY:

12622

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.115

Gnomad4 AMR

AF:

0.297

Gnomad4 ASJ

AF:

0.181

Gnomad4 EAS

AF:

0.324

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.159

Gnomad4 OTH

AF:

0.203

Alfa

AF:

0.175

Hom.:

2517

Bravo

AF:

0.182

Asia WGS

AF:

0.262

AC:

911

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.87

DANN

Benign

0.46

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