Variant 9-5260079-C-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 0.379 in 151,960 control chromosomes in the GnomAD database, including 12,678 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 0.38 ( 12678 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.11

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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.5260079C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57501

AN:

151842

Hom.:

12648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.343

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.350

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.351

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

GnomAD4 genome

AF:

0.379

AC:

57590

AN:

151960

Hom.:

12678

Cov.:

AF XY:

0.379

AC XY:

28164

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.613

Gnomad4 AMR

AF:

0.342

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.243

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.350

Gnomad4 NFE

AF:

0.274

Gnomad4 OTH

AF:

0.352

Alfa

AF:

0.234

Hom.:

844

Bravo

AF:

0.384

Asia WGS

AF:

0.303

AC:

1050

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

0.28

DANN

Benign

0.25

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