Variant 5-91268322-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 0.791 in 148,204 control chromosomes in the GnomAD database, including 47,330 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 0.79 ( 47330 hom., cov: 25)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.627

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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.91268322C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
LUCAT1	ENST00000647807.1 linkuse as main transcript	n.464-23312G>A	intron_variant
LUCAT1	ENST00000648385.1 linkuse as main transcript	n.367+45316G>A	intron_variant
LUCAT1	ENST00000648822.1 linkuse as main transcript	n.437-3609G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.791

AC:

117236

AN:

148128

Hom.:

47318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.664

Gnomad AMI

AF:

0.909

Gnomad AMR

AF:

0.745

Gnomad ASJ

AF:

0.910

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.754

Gnomad FIN

AF:

0.894

Gnomad MID

AF:

0.828

Gnomad NFE

AF:

0.877

Gnomad OTH

AF:

0.811

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

GnomAD4 genome

AF:

0.791

AC:

117278

AN:

148204

Hom.:

47330

Cov.:

AF XY:

0.789

AC XY:

56803

AN XY:

71952

show subpopulations

Gnomad4 AFR

AF:

0.664

Gnomad4 AMR

AF:

0.744

Gnomad4 ASJ

AF:

0.910

Gnomad4 EAS

AF:

0.536

Gnomad4 SAS

AF:

0.752

Gnomad4 FIN

AF:

0.894

Gnomad4 NFE

AF:

0.877

Gnomad4 OTH

AF:

0.810

Alfa

AF:

0.835

Hom.:

6674

Bravo

AF:

0.773

Asia WGS

AF:

0.657

AC:

2286

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

4.4

DANN

Benign

0.77

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