Variant rs10927101 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_033883.1(LINC02774):n.527-127C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,050 control chromosomes in the GnomAD database, including 15,216 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 0.44 ( 15213 hom., cov: 33)

Exomes 𝑓: 0.60 ( 3 hom. )

Consequence

LINC02774
NR_033883.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.323

Variant links:

Genes affected

LINC02774 (HGNC:27923): (long intergenic non-protein coding RNA 2774)

LINC02774 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02774	NR_033883.1 linkuse as main transcript	n.527-127C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02774	ENST00000440494.1 linkuse as main transcript	n.527-127C>A		intron_variant, non_coding_transcript_variant		1
LINC02774	ENST00000652928.1 linkuse as main transcript	n.259-127C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66691

AN:

151922

Hom.:

15197

Cov.:

show subpopulations

Gnomad AFR

AF:

0.512

Gnomad AMI

AF:

0.445

Gnomad AMR

AF:

0.471

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.682

Gnomad SAS

AF:

0.414

Gnomad FIN

AF:

0.399

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.448

GnomAD4 exome

AF:

0.600

AC:

AN:

Hom.:

AF XY:

0.600

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.439

AC:

66754

AN:

152040

Hom.:

15213

Cov.:

AF XY:

0.441

AC XY:

32748

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.512

Gnomad4 AMR

AF:

0.471

Gnomad4 ASJ

AF:

0.380

Gnomad4 EAS

AF:

0.682

Gnomad4 SAS

AF:

0.415

Gnomad4 FIN

AF:

0.399

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.450

Alfa

AF:

0.389

Hom.:

18634

Bravo

AF:

0.450

Asia WGS

AF:

0.557

AC:

1935

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.0

DANN

Benign

0.46

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