Variant 17-5733334-C-G 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 0.44 in 152,014 control chromosomes in the GnomAD database, including 14,846 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 0.44 ( 14846 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00400

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.5733334C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66900

AN:

151894

Hom.:

14835

Cov.:

show subpopulations

Gnomad AFR

AF:

0.419

Gnomad AMI

AF:

0.408

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.397

Gnomad NFE

AF:

0.457

Gnomad OTH

AF:

0.463

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

GnomAD4 genome

AF:

0.440

AC:

66941

AN:

152014

Hom.:

14846

Cov.:

AF XY:

0.437

AC XY:

32481

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.418

Gnomad4 AMR

AF:

0.497

Gnomad4 ASJ

AF:

0.503

Gnomad4 EAS

AF:

0.285

Gnomad4 SAS

AF:

0.430

Gnomad4 FIN

AF:

0.398

Gnomad4 NFE

AF:

0.457

Gnomad4 OTH

AF:

0.468

Alfa

AF:

0.172

Hom.:

231

Bravo

AF:

0.447

Asia WGS

AF:

0.386

AC:

1340

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

2.4

DANN

Benign

0.45

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