Variant rs34122827 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_126409.1(LINC00376):n.424-10117_424-10114del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 12344 hom., cov: 0)

Consequence

LINC00376
NR_126409.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.531

Variant links:

Genes affected

LINC00376 (HGNC:42701): (long intergenic non-protein coding RNA 376)

LINC00376 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00376	NR_126409.1 linkuse as main transcript	n.424-10117_424-10114del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00376	ENST00000439454.3 linkuse as main transcript	n.459-10117_459-10114del		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59244

AN:

151622

Hom.:

12347

Cov.:

show subpopulations

Gnomad AFR

AF:

0.304

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.360

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.0264

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.429

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.392

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

GnomAD4 genome

AF:

0.390

AC:

59246

AN:

151740

Hom.:

12344

Cov.:

AF XY:

0.381

AC XY:

28274

AN XY:

74138

show subpopulations

Gnomad4 AFR

AF:

0.304

Gnomad4 AMR

AF:

0.360

Gnomad4 ASJ

AF:

0.455

Gnomad4 EAS

AF:

0.0264

Gnomad4 SAS

AF:

0.387

Gnomad4 FIN

AF:

0.345

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.386

Alfa

AF:

0.436

Hom.:

1827

Bravo

AF:

0.385

Asia WGS

AF:

0.208

AC:

725

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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