Variant 6-91454381-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 0.54 in 151,872 control chromosomes in the GnomAD database, including 22,665 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 0.54 ( 22665 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.224

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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.91454381C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.540

AC:

81879

AN:

151754

Hom.:

22623

Cov.:

show subpopulations

Gnomad AFR

AF:

0.654

Gnomad AMI

AF:

0.363

Gnomad AMR

AF:

0.555

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.546

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.530

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.523

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

GnomAD4 genome

AF:

0.540

AC:

81968

AN:

151872

Hom.:

22665

Cov.:

AF XY:

0.542

AC XY:

40195

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.655

Gnomad4 AMR

AF:

0.555

Gnomad4 ASJ

AF:

0.589

Gnomad4 EAS

AF:

0.545

Gnomad4 SAS

AF:

0.429

Gnomad4 FIN

AF:

0.530

Gnomad4 NFE

AF:

0.476

Gnomad4 OTH

AF:

0.517

Alfa

AF:

0.519

Hom.:

2554

Bravo

AF:

0.547

Asia WGS

AF:

0.477

AC:

1656

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.6

DANN

Benign

0.88

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