Variant 14-87807501-G-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 0.661 in 151,944 control chromosomes in the GnomAD database, including 34,344 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 0.66 ( 34344 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.320

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.87807501G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258807	ENST00000554305.5 linkuse as main transcript	n.230+8631C>A		intron_variant		5
ENSG00000258807	ENST00000554519.1 linkuse as main transcript	n.120+8631C>A		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.661

AC:

100312

AN:

151826

Hom.:

34286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.807

Gnomad AMI

AF:

0.464

Gnomad AMR

AF:

0.714

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.885

Gnomad SAS

AF:

0.744

Gnomad FIN

AF:

0.605

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.556

Gnomad OTH

AF:

0.657

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

GnomAD4 genome

AF:

0.661

AC:

100433

AN:

151944

Hom.:

34344

Cov.:

AF XY:

0.667

AC XY:

49570

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.808

Gnomad4 AMR

AF:

0.715

Gnomad4 ASJ

AF:

0.500

Gnomad4 EAS

AF:

0.885

Gnomad4 SAS

AF:

0.745

Gnomad4 FIN

AF:

0.605

Gnomad4 NFE

AF:

0.556

Gnomad4 OTH

AF:

0.660

Alfa

AF:

0.577

Hom.:

32531

Bravo

AF:

0.673

Asia WGS

AF:

0.792

AC:

2753

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.3

DANN

Benign

0.40

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