Variant rs2894103 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_184064.1(LINC02636):n.1637G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,950 control chromosomes in the GnomAD database, including 19,428 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 0.50 ( 19428 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

LINC02636
NR_184064.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.126

Variant links:

Genes affected

LINC02636 (HGNC:54119): (long intergenic non-protein coding RNA 2636)

LINC02636 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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LINC02636	NR_184064.1 linkuse as main transcript	n.1637G>T	non_coding_transcript_exon_variant	2/4
LINC02636	NR_184065.1 linkuse as main transcript	n.1637G>T	non_coding_transcript_exon_variant	2/5
LINC02636	NR_184066.1 linkuse as main transcript	n.1637G>T	non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02636	ENST00000667615.1 linkuse as main transcript	n.423-62G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

76109

AN:

151828

Hom.:

19396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.537

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.582

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.659

Gnomad SAS

AF:

0.623

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.460

Gnomad OTH

AF:

0.502

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.501

AC:

76198

AN:

151946

Hom.:

19428

Cov.:

AF XY:

0.504

AC XY:

37426

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.537

Gnomad4 AMR

AF:

0.582

Gnomad4 ASJ

AF:

0.440

Gnomad4 EAS

AF:

0.658

Gnomad4 SAS

AF:

0.623

Gnomad4 FIN

AF:

0.406

Gnomad4 NFE

AF:

0.460

Gnomad4 OTH

AF:

0.504

Alfa

AF:

0.486

Hom.:

9024

Bravo

AF:

0.515

Asia WGS

AF:

0.633

AC:

2201

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.6

DANN

Benign

0.63

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