Variant chr17-55568879-T-C 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 0.175 in 152,114 control chromosomes in the GnomAD database, including 2,629 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 0.18 ( 2629 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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:

0.175

AC:

26622

AN:

151996

Hom.:

2625

Cov.:

show subpopulations

Gnomad AFR

AF:

0.110

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.238

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.192

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

GnomAD4 genome

AF:

0.175

AC:

26626

AN:

152114

Hom.:

2629

Cov.:

AF XY:

0.172

AC XY:

12824

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.110

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.226

Gnomad4 EAS

AF:

0.239

Gnomad4 SAS

AF:

0.148

Gnomad4 FIN

AF:

0.204

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.197

Hom.:

1906

Bravo

AF:

0.166

Asia WGS

AF:

0.180

AC:

627

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.5

DANN

Benign

0.75

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