Variant 5-135021015-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1

The variant allele was found at a frequency of 0.271 in 152,128 control chromosomes in the GnomAD database, including 5,953 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 0.27 ( 5953 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.56

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.17).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.135021015T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41135

AN:

152010

Hom.:

5950

Cov.:

show subpopulations

Gnomad AFR

AF:

0.209

Gnomad AMI

AF:

0.456

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.489

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.278

Gnomad OTH

AF:

0.261

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

GnomAD4 genome

AF:

0.271

AC:

41154

AN:

152128

Hom.:

5953

Cov.:

AF XY:

0.273

AC XY:

20281

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.209

Gnomad4 AMR

AF:

0.305

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.488

Gnomad4 SAS

AF:

0.384

Gnomad4 FIN

AF:

0.248

Gnomad4 NFE

AF:

0.278

Gnomad4 OTH

AF:

0.263

Alfa

AF:

0.279

Hom.:

8157

Bravo

AF:

0.270

Asia WGS

AF:

0.475

AC:

1650

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.17

CADD

Uncertain

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