Variant chr17-12665754-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The variant allele was found at a frequency of 0.375 in 158,126 control chromosomes in the GnomAD database, including 13,770 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 13574 hom., cov: 33)

Exomes 𝑓: 0.23 ( 196 hom. )

Consequence

Unknown

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.664

Variant links:

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ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 17-12665754-T-C is Benign according to our data. Variant chr17-12665754-T-C is described in ClinVar as [Benign]. Clinvar id is 1253022.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 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:

0.380

AC:

57738

AN:

152024

Hom.:

13526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.674

Gnomad AMI

AF:

0.224

Gnomad AMR

AF:

0.358

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.353

GnomAD4 exome

AF:

0.232

AC:

1391

AN:

5984

Hom.:

196

AF XY:

0.229

AC XY:

692

AN XY:

3020

show subpopulations

Gnomad4 AFR exome

AF:

0.629

Gnomad4 AMR exome

AF:

0.348

Gnomad4 ASJ exome

AF:

0.226

Gnomad4 EAS exome

AF:

0.190

Gnomad4 SAS exome

AF:

0.217

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.210

Gnomad4 OTH exome

AF:

0.231

GnomAD4 genome

AF:

0.380

AC:

57847

AN:

152142

Hom.:

13574

Cov.:

AF XY:

0.378

AC XY:

28125

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.675

Gnomad4 AMR

AF:

0.359

Gnomad4 ASJ

AF:

0.273

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.210

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.250

Gnomad4 OTH

AF:

0.350

Alfa

AF:

0.317

Hom.:

1257

Bravo

AF:

0.403

Asia WGS

AF:

0.229

AC:

799

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

This variant is associated with the following publications: (PMID: 18028454) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

8.2

DANN

Benign

0.32

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over