Variant 20-24077771-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 0.176 in 152,048 control chromosomes in the GnomAD database, including 4,680 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 0.18 ( 4680 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.620

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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.24077771C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01721	ENST00000664459.1 linkuse as main transcript	n.121+13263C>T		intron_variant
LINC01721	ENST00000669143.1 linkuse as main transcript	n.190+13263C>T		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26719

AN:

151930

Hom.:

4666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.451

Gnomad AMI

AF:

0.0835

Gnomad AMR

AF:

0.0937

Gnomad ASJ

AF:

0.0933

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.0358

Gnomad MID

AF:

0.169

Gnomad NFE

AF:

0.0592

Gnomad OTH

AF:

0.149

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

GnomAD4 genome

AF:

0.176

AC:

26776

AN:

152048

Hom.:

4680

Cov.:

AF XY:

0.173

AC XY:

12825

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.451

Gnomad4 AMR

AF:

0.0935

Gnomad4 ASJ

AF:

0.0933

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.124

Gnomad4 FIN

AF:

0.0358

Gnomad4 NFE

AF:

0.0592

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.0753

Hom.:

1401

Bravo

AF:

0.194

Asia WGS

AF:

0.195

AC:

677

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

2.3

DANN

Benign

0.38

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