Variant chr4-173840562-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 0.427 in 151,760 control chromosomes in the GnomAD database, including 15,166 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 0.43 ( 15166 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00400

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.173840562C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
LINC02269	ENST00000654333.1 linkuse as main transcript	n.318+6551C>T	intron_variant
LINC02269	ENST00000654653.1 linkuse as main transcript	n.230-15722C>T	intron_variant
LINC02269	ENST00000654916.1 linkuse as main transcript	n.230-15722C>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64720

AN:

151642

Hom.:

15165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.688

Gnomad AMR

AF:

0.508

Gnomad ASJ

AF:

0.441

Gnomad EAS

AF:

0.671

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.435

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.507

Gnomad OTH

AF:

0.424

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

GnomAD4 genome

AF:

0.427

AC:

64729

AN:

151760

Hom.:

15166

Cov.:

AF XY:

0.425

AC XY:

31509

AN XY:

74160

show subpopulations

Gnomad4 AFR

AF:

0.238

Gnomad4 AMR

AF:

0.508

Gnomad4 ASJ

AF:

0.441

Gnomad4 EAS

AF:

0.671

Gnomad4 SAS

AF:

0.308

Gnomad4 FIN

AF:

0.435

Gnomad4 NFE

AF:

0.507

Gnomad4 OTH

AF:

0.425

Alfa

AF:

0.452

Hom.:

6629

Bravo

AF:

0.432

Asia WGS

AF:

0.481

AC:

1673

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.0

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