Variant 5-79541733-A-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 0.546 in 152,248 control chromosomes in the GnomAD database, including 25,472 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 0.55 ( 25472 hom., cov: 34)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0250

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.79541733A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.546

AC:

83030

AN:

152130

Hom.:

25418

Cov.:

show subpopulations

Gnomad AFR

AF:

0.827

Gnomad AMI

AF:

0.536

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.375

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.392

Gnomad OTH

AF:

0.510

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

GnomAD4 genome

AF:

0.546

AC:

83146

AN:

152248

Hom.:

25472

Cov.:

AF XY:

0.549

AC XY:

40882

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.827

Gnomad4 AMR

AF:

0.558

Gnomad4 ASJ

AF:

0.375

Gnomad4 EAS

AF:

0.613

Gnomad4 SAS

AF:

0.357

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.392

Gnomad4 OTH

AF:

0.511

Alfa

AF:

0.343

Hom.:

1026

Bravo

AF:

0.567

Asia WGS

AF:

0.523

AC:

1822

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.1

DANN

Benign

0.53

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