Variant chr11-29580727-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_183754.1(LINC02755):n.125+13499T>C 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 0.517 in 151,782 control chromosomes in the GnomAD database, including 23,788 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 0.52 ( 23788 hom., cov: 32)

Consequence

LINC02755
NR_183754.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.178

Variant links:

Genes affected

LINC02755 (HGNC:54275): (long intergenic non-protein coding RNA 2755)

LINC02755 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02755	NR_183754.1 linkuse as main transcript	n.125+13499T>C		intron_variant, non_coding_transcript_variant
LINC02755	NR_183753.1 linkuse as main transcript	n.125+13499T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC02755	ENST00000657392.1 linkuse as main transcript	n.231+33368T>C	intron_variant, non_coding_transcript_variant
LINC02755	ENST00000525097.1 linkuse as main transcript	n.70+13499T>C	intron_variant, non_coding_transcript_variant	3
LINC02755	ENST00000528553.2 linkuse as main transcript	n.207+33368T>C	intron_variant, non_coding_transcript_variant	3
LINC02755	ENST00000653616.1 linkuse as main transcript	n.125+13499T>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.517

AC:

78400

AN:

151664

Hom.:

23744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.854

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.351

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.257

Gnomad SAS

AF:

0.396

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.414

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.496

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

GnomAD4 genome

AF:

0.517

AC:

78496

AN:

151782

Hom.:

23788

Cov.:

AF XY:

0.507

AC XY:

37626

AN XY:

74168

show subpopulations

Gnomad4 AFR

AF:

0.854

Gnomad4 AMR

AF:

0.351

Gnomad4 ASJ

AF:

0.431

Gnomad4 EAS

AF:

0.257

Gnomad4 SAS

AF:

0.395

Gnomad4 FIN

AF:

0.354

Gnomad4 NFE

AF:

0.408

Gnomad4 OTH

AF:

0.500

Alfa

AF:

0.459

Hom.:

2686

Bravo

AF:

0.530

Asia WGS

AF:

0.376

AC:

1303

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

1.3

DANN

Benign

0.69

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