Variant 5-170145727-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 0.328 in 151,972 control chromosomes in the GnomAD database, including 8,877 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 ( 8877 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.57

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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.407 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:

0.328

AC:

49822

AN:

151854

Hom.:

8881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.177

Gnomad AMI

AF:

0.471

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.366

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.331

Gnomad FIN

AF:

0.320

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.411

Gnomad OTH

AF:

0.306

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

GnomAD4 genome

AF:

0.328

AC:

49807

AN:

151972

Hom.:

8877

Cov.:

AF XY:

0.326

AC XY:

24218

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.177

Gnomad4 AMR

AF:

0.358

Gnomad4 ASJ

AF:

0.366

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.330

Gnomad4 FIN

AF:

0.320

Gnomad4 NFE

AF:

0.411

Gnomad4 OTH

AF:

0.302

Alfa

AF:

0.388

Hom.:

8098

Bravo

AF:

0.323

Asia WGS

AF:

0.314

AC:

1088

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.64

DANN

Benign

0.95

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