Variant rs7662358 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000503580.1(LINC01060):n.88-11016C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 151,484 control chromosomes in the GnomAD database, including 2,069 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 0.16 ( 2069 hom., cov: 32)

Consequence

LINC01060
ENST00000503580.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.408

Variant links:

Genes affected

LINC01060 (HGNC:49081): (long intergenic non-protein coding RNA 1060)

LINC01060 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01060	ENST00000503580.1 link	n.88-11016C>A	intron_variant	3
LINC01060	ENST00000664177.1 link	n.331-10578C>A	intron_variant
LINC01060	ENST00000692519.1 link	n.362-10578C>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24569

AN:

151366

Hom.:

2064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0828

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.175

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.170

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

GnomAD4 genome

AF:

0.162

AC:

24599

AN:

151484

Hom.:

2069

Cov.:

AF XY:

0.158

AC XY:

11664

AN XY:

74000

show subpopulations

Gnomad4 AFR

AF:

0.186

Gnomad4 AMR

AF:

0.145

Gnomad4 ASJ

AF:

0.0828

Gnomad4 EAS

AF:

0.107

Gnomad4 SAS

AF:

0.117

Gnomad4 FIN

AF:

0.139

Gnomad4 NFE

AF:

0.168

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.155

Hom.:

2130

Bravo

AF:

0.161

Asia WGS

AF:

0.119

AC:

412

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.3

DANN

Benign

0.76

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