Variant rs5755393 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_138042.1(LINC02885):n.460+16789T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,174 control chromosomes in the GnomAD database, including 31,292 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 0.62 ( 31292 hom., cov: 32)

Consequence

LINC02885
NR_138042.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.795

Variant links:

Genes affected

LINC02885 (HGNC:41188): (long intergenic non-protein coding RNA 2885)

LINC02885 links:

LOC124905109 (HGNC:):

LOC124905109 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02885	NR_138042.1 link	n.460+16789T>C		intron_variant
LOC124905109	XR_007068083.1 link	n.85+3094T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
LINC02885	ENST00000665218.1 link	n.157+3094T>C	intron_variant
LINC02885	ENST00000668433.1 link	n.343+21576T>C	intron_variant
LINC02885	ENST00000700833.1 link	n.261+3094T>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.620

AC:

94259

AN:

152056

Hom.:

31251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.882

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.542

Gnomad ASJ

AF:

0.596

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.504

Gnomad FIN

AF:

0.412

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.532

Gnomad OTH

AF:

0.596

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

GnomAD4 genome

AF:

0.620

AC:

94338

AN:

152174

Hom.:

31292

Cov.:

AF XY:

0.612

AC XY:

45486

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.882

Gnomad4 AMR

AF:

0.541

Gnomad4 ASJ

AF:

0.596

Gnomad4 EAS

AF:

0.470

Gnomad4 SAS

AF:

0.504

Gnomad4 FIN

AF:

0.412

Gnomad4 NFE

AF:

0.532

Gnomad4 OTH

AF:

0.589

Alfa

AF:

0.581

Hom.:

4553

Bravo

AF:

0.641

Asia WGS

AF:

0.461

AC:

1607

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.13

DANN

Benign

0.40

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