Variant rs7480010 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_038309.1(LINC02740):n.332+12925C>T 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 0.562 in 152,054 control chromosomes in the GnomAD database, including 29,537 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 0.56 ( 29537 hom., cov: 33)

Consequence

LINC02740
NR_038309.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.614

Variant links:

Genes affected

LINC02740 (HGNC:54257): (long intergenic non-protein coding RNA 2740)

LINC02740 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02740	NR_038309.1 linkuse as main transcript	n.332+12925C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC02740	ENST00000658612.1 linkuse as main transcript	n.509+12925C>T	intron_variant, non_coding_transcript_variant
LINC02740	ENST00000525641.5 linkuse as main transcript	n.177+12925C>T	intron_variant, non_coding_transcript_variant	3
LINC02740	ENST00000527757.2 linkuse as main transcript	n.355-10182C>T	intron_variant, non_coding_transcript_variant	3
LINC02740	ENST00000530387.5 linkuse as main transcript	n.93+12925C>T	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.562

AC:

85443

AN:

151938

Hom.:

29539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.530

Gnomad AMR

AF:

0.713

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.803

Gnomad SAS

AF:

0.606

Gnomad FIN

AF:

0.832

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.723

Gnomad OTH

AF:

0.585

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

GnomAD4 genome

AF:

0.562

AC:

85444

AN:

152054

Hom.:

29537

Cov.:

AF XY:

0.571

AC XY:

42417

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.713

Gnomad4 ASJ

AF:

0.595

Gnomad4 EAS

AF:

0.803

Gnomad4 SAS

AF:

0.607

Gnomad4 FIN

AF:

0.832

Gnomad4 NFE

AF:

0.723

Gnomad4 OTH

AF:

0.586

Alfa

AF:

0.688

Hom.:

76918

Bravo

AF:

0.535

Asia WGS

AF:

0.627

AC:

2180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.14

DANN

Benign

0.70

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